diff --git a/script/upstream/merge.ts b/script/upstream/merge.ts
index e4ac18f7441..77f3faa4713 100644
--- a/script/upstream/merge.ts
+++ b/script/upstream/merge.ts
@@ -548,6 +548,10 @@ async function main() {
   logger.step(7, 8, "Merging into Kilo branch...")
 
   await git.checkout(kiloBranch)
+  if (prior) {
+    const linked = await git.recordAncestor(targetVersion.commit, `merge: record upstream ${targetVersion.tag}`)
+    if (linked) logger.info(`Recorded upstream ${targetVersion.tag} as Kilo branch ancestry`)
+  }
   const mergeResult = await git.merge(opencodeBranch)
 
   if (!mergeResult.success) {
diff --git a/script/upstream/utils/git.test.ts b/script/upstream/utils/git.test.ts
index f841d74bf59..7d1f5e3c904 100644
--- a/script/upstream/utils/git.test.ts
+++ b/script/upstream/utils/git.test.ts
@@ -3,7 +3,16 @@ import { mkdtemp, rm } from "node:fs/promises"
 import { join } from "node:path"
 import { tmpdir } from "node:os"
 import { $ } from "bun"
-import { createCommit, findLatestCompatCommit, getCommitHash, getCommitParents, updateBranch, writeTree } from "./git"
+import {
+  createCommit,
+  findLatestCompatCommit,
+  getCommitHash,
+  getCommitParents,
+  isAncestor,
+  recordAncestor,
+  updateBranch,
+  writeTree,
+} from "./git"
 
 const cwd = process.cwd()
 let dir = ""
@@ -51,8 +60,21 @@ test("finds previous compatibility commit for transformed base", async () => {
   const tree = await writeTree()
   const next = await createCommit(tree, "refactor: kilo compat for v1.0.1", prior)
   await updateBranch("opencode-v1.0.1", next)
-
   const base = (await $`git merge-base main opencode-v1.0.1`.text()).trim()
   expect(base).toBe(prior)
   expect(await getCommitParents(next)).toEqual([prior])
+
+  await $`git checkout main`.quiet()
+  expect(await recordAncestor(target, "merge: record upstream v1.0.1")).toBe(true)
+  const link = await getCommitHash("HEAD")
+  expect(await getCommitParents(link)).toEqual([prior, target])
+  expect(await isAncestor(target, link)).toBe(true)
+
+  const linked = (await $`git merge-base main opencode-v1.0.1`.text()).trim()
+  expect(linked).toBe(prior)
+
+  await $`git merge opencode-v1.0.1`.quiet()
+  const head = await getCommitHash("HEAD")
+  expect(await getCommitParents(head)).toEqual([link, next])
+  expect(await isAncestor(target, head)).toBe(true)
 })
diff --git a/script/upstream/utils/git.ts b/script/upstream/utils/git.ts
index d8730d2d378..35588124e00 100644
--- a/script/upstream/utils/git.ts
+++ b/script/upstream/utils/git.ts
@@ -205,6 +205,16 @@ export async function updateBranch(name: string, commit: string): Promise<void>
   await $`git update-ref refs/heads/${name} ${commit}`
 }
 
+export async function recordAncestor(ref: string, message: string): Promise<boolean> {
+  if (await isAncestor(ref, "HEAD")) return false
+
+  const result = await $`git merge -s ours --no-ff ${ref} -m ${message}`.nothrow()
+  if (result.exitCode !== 0) {
+    throw new Error(`Failed to record ancestor ${ref}: ${result.stderr.toString()}`)
+  }
+  return true
+}
+
 async function compatUpstream(message: string): Promise<string | null> {
   const prefix = "refactor: kilo compat for "
   if (!message.startsWith(prefix)) return null