diff --git a/src/Bridge.ts b/src/Bridge.ts
index 0d15728f..4a7ddad0 100644
--- a/src/Bridge.ts
+++ b/src/Bridge.ts
@@ -789,7 +789,7 @@ export class Bridge {
                 try {
                     await (
                         new SetupConnection(
-                            roomId, this.as, this.tokenStore, this.config, 
+                            roomId, this.as, this.tokenStore, this.storage, this.config, 
                             this.getOrCreateAdminRoom.bind(this),
                             this.github,
                         )
diff --git a/src/ConnectionManager.ts b/src/ConnectionManager.ts
index 5256b2e9..98f159e2 100644
--- a/src/ConnectionManager.ts
+++ b/src/ConnectionManager.ts
@@ -96,7 +96,7 @@ export class ConnectionManager {
             if (!this.config.checkPermission(userId, "github", BridgePermissionLevel.manageConnections)) {
                 throw new ApiError('User is not permitted to provision connections for GitHub', ErrCode.ForbiddenUser);
             }
-            const res = await GitHubRepoConnection.provisionConnection(roomId, userId, data, this.as, this.tokenStore, this.github, this.config.github);
+            const res = await GitHubRepoConnection.provisionConnection(roomId, userId, data, this.as, this.tokenStore, this.github, this.config.github, this.storage);
             await this.as.botIntent.underlyingClient.sendStateEvent(roomId, GitHubRepoConnection.CanonicalEventType, res.connection.stateKey, res.stateEventContent);
             this.push(res.connection);
             return res.connection;
@@ -145,7 +145,7 @@ export class ConnectionManager {
                 throw Error('GitHub is not configured');
             }
             this.assertStateAllowed(state, "github");
-            return new GitHubRepoConnection(roomId, this.as, state.content, this.tokenStore, state.stateKey, this.github, this.config.github);
+            return new GitHubRepoConnection(roomId, this.as, state.content, this.tokenStore, this.storage, state.stateKey, this.github, this.config.github);
         }
 
         if (GitHubDiscussionConnection.EventTypes.includes(state.type)) {
diff --git a/src/Connections/GithubRepo.ts b/src/Connections/GithubRepo.ts
index 179c3fde..f399bf26 100644
--- a/src/Connections/GithubRepo.ts
+++ b/src/Connections/GithubRepo.ts
@@ -21,6 +21,7 @@ import { BridgeConfigGitHub } from "../Config/Config";
 import { ApiError, ErrCode } from "../api";
 import { PermissionCheckFn } from ".";
 import { MinimalGitHubIssue, MinimalGitHubRepo } from "../libRs";
+import { IBridgeStorageProvider } from "../Stores/StorageProvider";
 const log = new LogWrapper("GitHubRepoConnection");
 const md = new markdown();
 
@@ -48,6 +49,7 @@ export interface GitHubRepoConnectionOptions extends IConnectionState {
     newIssue?: {
         labels: string[];
     };
+    useThreads?: boolean;
 }
 export interface GitHubRepoConnectionState extends GitHubRepoConnectionOptions {
     org: string;
@@ -150,7 +152,7 @@ function validateState(state: Record<string, unknown>): GitHubRepoConnectionStat
  */
 export class GitHubRepoConnection extends CommandConnection implements IConnection {
     static async provisionConnection(roomId: string, userId: string, data: Record<string, unknown>, as: Appservice,
-        tokenStore: UserTokenStore, githubInstance: GithubInstance, config: BridgeConfigGitHub) {
+        tokenStore: UserTokenStore, githubInstance: GithubInstance, config: BridgeConfigGitHub, store: IBridgeStorageProvider) {
         const validData = validateState(data);
         const octokit = await tokenStore.getOctokitForUser(userId);
         if (!octokit) {
@@ -183,7 +185,7 @@ export class GitHubRepoConnection extends CommandConnection implements IConnecti
         const stateEventKey = `${validData.org}/${validData.repo}`;
         return {
             stateEventContent: validData,
-            connection: new GitHubRepoConnection(roomId, as, validData, tokenStore, stateEventKey, githubInstance, config),
+            connection: new GitHubRepoConnection(roomId, as, validData, tokenStore, store, stateEventKey, githubInstance, config),
         }
     }
 
@@ -281,6 +283,7 @@ export class GitHubRepoConnection extends CommandConnection implements IConnecti
         private readonly as: Appservice,
         private state: GitHubRepoConnectionState,
         private readonly tokenStore: UserTokenStore,
+        private readonly store: IBridgeStorageProvider,
         stateKey: string,
         private readonly githubInstance: GithubInstance,
         private readonly config: BridgeConfigGitHub,
@@ -297,6 +300,32 @@ export class GitHubRepoConnection extends CommandConnection implements IConnecti
             );
     }
 
+    protected async setThreadForRemoteId(eventId: string, remoteId: string|number) {
+        // Store regardless of configuration, in case the user wants to turn it on.
+        await this.store.setEventIdForRemoteId(`${this.connectionId}/${remoteId}`, eventId);
+        log.debug(`Stored thread eventId for ${remoteId} as ${eventId}`);
+    }
+
+    protected async getThreadForRemoteId(remoteId: string|number, renderInTimeline = false): Promise<Record<string, unknown>|undefined> {
+        const parentEventId = this.state.useThreads && await this.store.getEventIdForRemoteId(`${this.connectionId}/${remoteId}`);
+        log.debug(`Found ${parentEventId || "no eventId"} for ${remoteId}`);
+        if (!parentEventId) {
+            return;
+        }
+
+        return { 
+            "m.relates_to": {
+                rel_type: renderInTimeline ? undefined : "m.thread",
+                event_id: parentEventId,
+                // Needed to prevent clients from showing these as actual replies
+                is_falling_back: true,
+                "m.in_reply_to": {
+                    event_id: parentEventId,
+                }
+            },
+        }
+    }
+
     public get hotlinkIssues() {
         const cfg = this.config.defaultOptions?.hotlinkIssues || this.state.hotlinkIssues;
         if (cfg === false) {
@@ -582,13 +611,14 @@ export class GitHubRepoConnection extends CommandConnection implements IConnecti
         }
         const content = emoji.emojify(message);
         const labels = FormatUtil.formatLabels(event.issue.labels?.map(l => ({ name: l.name, description: l.description || undefined, color: l.color || undefined }))); 
-        await this.as.botIntent.sendEvent(this.roomId, {
+        const eventId = await this.as.botIntent.sendEvent(this.roomId, {
             msgtype: "m.notice",
             body: content + (labels.plain.length > 0 ? ` with labels ${labels.plain}`: ""),
             formatted_body: md.renderInline(content) + (labels.html.length > 0 ? ` with labels ${labels.html}`: ""),
             format: "org.matrix.custom.html",
             ...FormatUtil.getPartialBodyForGithubIssue(event.repository, event.issue),
         });
+        await this.setThreadForRemoteId(eventId, event.issue.id);
     }
 
     public async onIssueStateChange(event: IssuesEditedEvent|IssuesReopenedEvent|IssuesClosedEvent) {
@@ -628,13 +658,18 @@ export class GitHubRepoConnection extends CommandConnection implements IConnecti
             }
         }
         const content = `**${event.sender.login}** ${state} issue [${orgRepoName}#${event.issue.number}](${event.issue.html_url}): "${emoji.emojify(event.issue.title)}"${withComment}`;
-        await this.as.botIntent.sendEvent(this.roomId, {
+        const thread = await this.getThreadForRemoteId(event.issue.id, true);
+        const eventId = await this.as.botIntent.sendEvent(this.roomId, {
             msgtype: "m.notice",
             body: content,
             formatted_body: md.renderInline(content),
             format: "org.matrix.custom.html",
+            ...thread,
             ...FormatUtil.getPartialBodyForGithubIssue(event.repository, event.issue),
         });
+        if (!thread) {
+            this.setThreadForRemoteId(eventId, event.issue.id);
+        }
     }
 
     public async onIssueEdited(event: IssuesEditedEvent) {
@@ -647,13 +682,18 @@ export class GitHubRepoConnection extends CommandConnection implements IConnecti
         log.info(`onIssueEdited ${this.roomId} ${this.org}/${this.repo} #${event.issue.number}`);
         const orgRepoName = event.repository.full_name;
         const content = `**${event.sender.login}** edited issue [${orgRepoName}#${event.issue.number}](${event.issue.html_url}): "${emoji.emojify(event.issue.title)}"`;
-        await this.as.botIntent.sendEvent(this.roomId, {
+        const thread = await this.getThreadForRemoteId(event.issue.id);
+        const eventId = await this.as.botIntent.sendEvent(this.roomId, {
             msgtype: "m.notice",
             body: content,
             formatted_body: md.renderInline(content),
             format: "org.matrix.custom.html",
+            ...thread,
             ...FormatUtil.getPartialBodyForGithubIssue(event.repository, event.issue),
         });
+        if (!thread) {
+            this.setThreadForRemoteId(eventId, event.issue.id);
+        }
     }
 
     public async onIssueLabeled(event: IssuesLabeledEvent) {
@@ -678,12 +718,15 @@ export class GitHubRepoConnection extends CommandConnection implements IConnecti
             const orgRepoName = event.repository.full_name;
             const {plain, html} = FormatUtil.formatLabels(event.issue.labels?.map(l => ({ name: l.name, description: l.description || undefined, color: l.color || undefined }))); 
             const content = `**${event.sender.login}** labeled issue [${orgRepoName}#${event.issue.number}](${event.issue.html_url}): "${emoji.emojify(event.issue.title)}"`;
-            this.as.botIntent.sendEvent(this.roomId, {
-                msgtype: "m.notice",
-                body: content + (plain.length > 0 ? ` with labels ${plain}`: ""),
-                formatted_body: md.renderInline(content) + (html.length > 0 ? ` with labels ${html}`: ""),
-                format: "org.matrix.custom.html",
-                ...FormatUtil.getPartialBodyForGithubIssue(event.repository, event.issue),
+            this.getThreadForRemoteId(event.issue.id).then((thread) => {
+                return this.as.botIntent.sendEvent(this.roomId, {
+                    msgtype: "m.notice",
+                    body: content + (plain.length > 0 ? ` with labels ${plain}`: ""),
+                    formatted_body: md.renderInline(content) + (html.length > 0 ? ` with labels ${html}`: ""),
+                    format: "org.matrix.custom.html",
+                    ...thread,
+                    ...FormatUtil.getPartialBodyForGithubIssue(event.repository, event.issue),
+                })
             }).catch(ex  => {
                 log.error('Failed to send onIssueLabeled message', ex);
             });
@@ -736,14 +779,19 @@ export class GitHubRepoConnection extends CommandConnection implements IConnecti
         }
         const content = emoji.emojify(`**${event.sender.login}** ${verb} a new PR [${orgRepoName}#${event.pull_request.number}](${event.pull_request.html_url}): "${event.pull_request.title}"`);
         const labels = FormatUtil.formatLabels(event.pull_request.labels?.map(l => ({ name: l.name, description: l.description || undefined, color: l.color || undefined })));  
-        await this.as.botIntent.sendEvent(this.roomId, {
+        const thread = await this.getThreadForRemoteId(event.pull_request.id);
+        const eventId = await this.as.botIntent.sendEvent(this.roomId, {
             msgtype: "m.notice",
             body: content + (labels.plain.length > 0 ? ` with labels ${labels}`: "") + diffContent,
             formatted_body: md.renderInline(content) + (labels.html.length > 0 ? ` with labels ${labels.html}`: "") + diffContentHtml,
             format: "org.matrix.custom.html",
+            ...thread,
             ...FormatUtil.getPartialBodyForGithubIssue(event.repository, event.pull_request),
             ...FormatUtil.getPartialBodyForGitHubPR(event.repository, event.pull_request),
         });
+        if (!thread) {
+            this.setThreadForRemoteId(eventId, event.pull_request.id);
+        }
     }
 
     public async onPRReadyForReview(event: PullRequestReadyForReviewEvent) {
@@ -759,14 +807,18 @@ export class GitHubRepoConnection extends CommandConnection implements IConnecti
         }
         const orgRepoName = event.repository.full_name;
         const content = emoji.emojify(`**${event.sender.login}** has marked [${orgRepoName}#${event.pull_request.number}](${event.pull_request.html_url}) as ready to review "${event.pull_request.title}"`);
-        await this.as.botIntent.sendEvent(this.roomId, {
+        const thread = await this.getThreadForRemoteId(event.pull_request.id, true);
+        const eventId = await this.as.botIntent.sendEvent(this.roomId, {
             msgtype: "m.notice",
             body: content,
             formatted_body: md.renderInline(content),
             format: "org.matrix.custom.html",
-            // TODO: Fix types.
+            ...thread,
             ...FormatUtil.getPartialBodyForGithubIssue(event.repository, event.pull_request),
         });
+        if (!thread) {
+            this.setThreadForRemoteId(eventId, event.pull_request.id);
+        }
     }
 
     public async onPRReviewed(event: PullRequestReviewSubmittedEvent) {
@@ -792,14 +844,18 @@ export class GitHubRepoConnection extends CommandConnection implements IConnecti
             return;
         }
         const content = emoji.emojify(`**${event.sender.login}** ${emojiForReview} ${event.review.state.toLowerCase()} [${orgRepoName}#${event.pull_request.number}](${event.pull_request.html_url}) "${event.pull_request.title}"`);
-        await this.as.botIntent.sendEvent(this.roomId, {
+        const thread = await this.getThreadForRemoteId(event.pull_request.id, true);
+        const eventId = await this.as.botIntent.sendEvent(this.roomId, {
             msgtype: "m.notice",
             body: content,
             formatted_body: md.renderInline(content),
             format: "org.matrix.custom.html",
-            // TODO: Fix types.
+            ...thread,
             ...FormatUtil.getPartialBodyForGithubIssue(event.repository, event.pull_request),
         });
+        if (!thread) {
+            this.setThreadForRemoteId(eventId, event.pull_request.id);
+        }
     }
 
     public async onPRClosed(event: PullRequestClosedEvent) {
@@ -838,11 +894,13 @@ export class GitHubRepoConnection extends CommandConnection implements IConnecti
         }
 
         const content = emoji.emojify(`**${event.sender.login}** ${verb} PR [${orgRepoName}#${event.pull_request.number}](${event.pull_request.html_url}): "${event.pull_request.title}"${withComment}`);
+        const thread = await this.getThreadForRemoteId(event.pull_request.id, true);
         await this.as.botIntent.sendEvent(this.roomId, {
             msgtype: "m.notice",
             body: content,
             formatted_body: md.renderInline(content),
             format: "org.matrix.custom.html",
+            ...thread,
             // TODO: Fix types.
             ...FormatUtil.getPartialBodyForGithubIssue(event.repository, event.pull_request),
         });
diff --git a/src/Connections/SetupConnection.ts b/src/Connections/SetupConnection.ts
index 2293f002..da13b3b8 100644
--- a/src/Connections/SetupConnection.ts
+++ b/src/Connections/SetupConnection.ts
@@ -13,6 +13,7 @@ import { FigmaFileConnection } from "./FigmaFileConnection";
 import { URL } from "url";
 import { SetupWidget } from "../Widgets/SetupWidget";
 import { AdminRoom } from "../AdminRoom";
+import { IBridgeStorageProvider } from "../Stores/StorageProvider";
 const md = new markdown();
 
 /**
@@ -27,6 +28,7 @@ export class SetupConnection extends CommandConnection {
     constructor(public readonly roomId: string,
         private readonly as: Appservice,
         private readonly tokenStore: UserTokenStore,
+        private readonly store: IBridgeStorageProvider,
         private readonly config: BridgeConfig,
         private readonly getOrCreateAdminRoom: (userId: string) => Promise<AdminRoom>,
         private readonly githubInstance?: GithubInstance,) {
@@ -73,7 +75,7 @@ export class SetupConnection extends CommandConnection {
             throw new CommandError("Invalid GitHub url", "The GitHub url you entered was not valid.");
         }
         const [, org, repo] = urlParts;
-        const res = await GitHubRepoConnection.provisionConnection(this.roomId, userId, {org, repo}, this.as, this.tokenStore, this.githubInstance, this.config.github);
+        const res = await GitHubRepoConnection.provisionConnection(this.roomId, userId, {org, repo}, this.as, this.tokenStore, this.githubInstance, this.config.github, this.store);
         await this.as.botClient.sendStateEvent(this.roomId, GitHubRepoConnection.CanonicalEventType, url, res.stateEventContent);
         await this.as.botClient.sendNotice(this.roomId, `Room configured to bridge ${org}/${repo}`);
     }
diff --git a/src/Stores/MemoryStorageProvider.ts b/src/Stores/MemoryStorageProvider.ts
index 6f4cd7fb..281dc957 100644
--- a/src/Stores/MemoryStorageProvider.ts
+++ b/src/Stores/MemoryStorageProvider.ts
@@ -2,6 +2,7 @@ import { MemoryStorageProvider as MSP } from "matrix-bot-sdk";
 import { IBridgeStorageProvider } from "./StorageProvider";
 import { IssuesGetResponseData } from "../Github/Types";
 import { ProvisionSession } from "matrix-appservice-bridge";
+import QuickLRU from "@alloc/quick-lru";
 
 export class MemoryStorageProvider extends MSP implements IBridgeStorageProvider {
     private issues: Map<string, IssuesGetResponseData> = new Map();
@@ -10,6 +11,9 @@ export class MemoryStorageProvider extends MSP implements IBridgeStorageProvider
     private figmaCommentIds: Map<string, string> = new Map();
     private widgetSessions: Map<string, ProvisionSession> = new Map();
 
+    // Set to a suitably large, but bounded size.
+    private eventIdForRemoteId = new QuickLRU<string, string>({ maxSize: 5000 });
+
     constructor() {
         super();
     }
@@ -54,16 +58,26 @@ export class MemoryStorageProvider extends MSP implements IBridgeStorageProvider
     public async getSessionForToken(token: string) {
        return this.widgetSessions.get(token) || null;
     }
+
     public async createSession(session: ProvisionSession) {
         this.widgetSessions.set(session.token, session);
     }
+
     public async  deleteSession(token: string) {
         this.widgetSessions.delete(token);
     }
+
     public async deleteAllSessions(userId: string) {
         [...this.widgetSessions.values()]
             .filter(s => s.userId === userId)
             .forEach(s => this.widgetSessions.delete(s.token));
     }
 
+    public async getEventIdForRemoteId(remoteId: string) {
+        return this.eventIdForRemoteId.get(remoteId) ?? null;
+    }
+
+    public async setEventIdForRemoteId(remoteId: string, eventId: string) {
+        this.eventIdForRemoteId.set(remoteId, eventId);
+    }
 }
diff --git a/src/Stores/RedisStorageProvider.ts b/src/Stores/RedisStorageProvider.ts
index bb982d5c..9815762c 100644
--- a/src/Stores/RedisStorageProvider.ts
+++ b/src/Stores/RedisStorageProvider.ts
@@ -15,9 +15,12 @@ const GH_ISSUES_KEY = "gh.issues";
 const GH_ISSUES_LAST_COMMENT_KEY = "gh.issues.last_comment";
 const GH_ISSUES_REVIEW_DATA_KEY = "gh.issues.review_data";
 const FIGMA_EVENT_COMMENT_ID = "figma.comment_event_id";
+const REMOTE_EVENTS_HASH = "remote_events";
+const REMOTE_EVENTS_LRU = "remote_events_lru";
 const COMPLETED_TRANSACTIONS_EXPIRE_AFTER = 24 * 60 * 60; // 24 hours
 const ISSUES_EXPIRE_AFTER = 7 * 24 * 60 * 60; // 7 days
 const ISSUES_LAST_COMMENT_EXPIRE_AFTER = 14 * 24 * 60 * 60; // 7 days
+const REMOTE_EVENTS_MAX_SIZE = 5000;
 
 
 const WIDGET_TOKENS = "widgets.tokens.";
@@ -155,4 +158,23 @@ export class RedisStorageProvider implements IBridgeStorageProvider {
             token = await this.redis.spop(`${WIDGET_USER_TOKENS}${userId}`);
         }
     }
+
+    async getEventIdForRemoteId(remoteId: string): Promise<string|null> {
+        const result = await this.redis.hget(REMOTE_EVENTS_HASH, remoteId);
+        if (result) {
+            await this.redis.zadd(REMOTE_EVENTS_LRU, Date.now(), remoteId);
+        }
+        return result;
+    }
+
+    async setEventIdForRemoteId(remoteId: string, eventId: string): Promise<void> {
+        await this.redis.hset(REMOTE_EVENTS_HASH, remoteId, eventId);
+        await this.redis.zadd(REMOTE_EVENTS_LRU, Date.now(), remoteId);
+        const lruCount = await this.redis.zcount(REMOTE_EVENTS_LRU, "-inf", "+inf");
+        if (lruCount <= REMOTE_EVENTS_MAX_SIZE) {
+            return;
+        }
+        const popped = await this.redis.zpopmin(REMOTE_EVENTS_LRU, lruCount - REMOTE_EVENTS_MAX_SIZE);
+        await this.redis.zrem(REMOTE_EVENTS_HASH, popped);
+    }
 }
diff --git a/src/Stores/StorageProvider.ts b/src/Stores/StorageProvider.ts
index 52ff39da..aaa61160 100644
--- a/src/Stores/StorageProvider.ts
+++ b/src/Stores/StorageProvider.ts
@@ -11,4 +11,6 @@ export interface IBridgeStorageProvider extends IAppserviceStorageProvider, ISto
     getPRReviewData(repo: string, issueNumber: string, scope?: string): Promise<any|null>;
     setFigmaCommentEventId(roomId: string, figmaCommentId: string, eventId: string): Promise<void>;
     getFigmaCommentEventId(roomId: string, figmaCommentId: string): Promise<string|null>;
+    setEventIdForRemoteId(remoteId: string, eventId: string): Promise<void>;
+    getEventIdForRemoteId(remoteId: string): Promise<string|null>;
 }
\ No newline at end of file