diff --git a/core/targethasher/BUILD.bazel b/core/targethasher/BUILD.bazel
index 7b304093..590517a1 100644
--- a/core/targethasher/BUILD.bazel
+++ b/core/targethasher/BUILD.bazel
@@ -23,6 +23,7 @@ go_test(
     srcs = [
         "graph_rapid_test.go",
         "graph_test.go",
+        "markers_test.go",
         "mock_sourcehasher_test.go",
         "sourcehasher_test.go",
     ],
diff --git a/core/targethasher/graph.go b/core/targethasher/graph.go
index f37f4330..51a22211 100644
--- a/core/targethasher/graph.go
+++ b/core/targethasher/graph.go
@@ -438,9 +438,11 @@ func shouldCollapseToBzlmodRepo(target *Target, repo string, fullHashRepos set.S
 //
 // Marker files track both the repo rule's declarative inputs (version,
 // URL, integrity) and per-file SHA-256 content hashes for local patches
-// applied via single_version_override. readMarkerHash hashes all stable
-// lines (skipping ENV) so the collapsed hash changes on dependency
-// upgrades AND patch content modifications.
+// applied via single_version_override. readMarkerHash hashes the first line
+// and the main-repo FILE: lines only (skipping ENV, REPO_MAPPING and FILE:
+// lines for other repos, which can embed the output_base path) so the
+// collapsed hash changes on dependency upgrades AND patch content
+// modifications.
 //
 // Every external repo referenced in the query result should have a
 // marker file after bazel query completes. Returns an error if a
diff --git a/core/targethasher/markers.go b/core/targethasher/markers.go
index 3805fb70..dd5cd1df 100644
--- a/core/targethasher/markers.go
+++ b/core/targethasher/markers.go
@@ -29,7 +29,8 @@ import (
 // external repo marker files and returns a map from canonical repo name
 // to a hash derived from the stable lines of each marker file.
 // This hash changes whenever the repo's version, URL, or patch file
-// contents change. ENV lines are excluded for cross-environment stability.
+// contents change. See readMarkerHash for the lines that are excluded for
+// cross-environment and cross-workspace stability.
 func ReadRepoMarkerHashes(ctx context.Context, workspacePath, bazelCommand string) (map[string][]byte, error) {
 	outputBase, err := bazel.OutputBase(ctx, workspacePath, bazelCommand)
 	if err != nil {
@@ -66,12 +67,35 @@ func ReadRepoMarkerHashes(ctx context.Context, workspacePath, bazelCommand strin
 	return hashes, nil
 }
 
+// localInputPrefixes mark the marker lines for inputs that live in the main
+// repo. Bazel records a repo rule's file-system inputs as KIND:@@<repo>//<path>
+// (the main repo's canonical name is empty), where KIND is FILE for a file,
+// DIRTREE for a directory tree and DIRENTS for a directory listing. Main-repo
+// inputs are checked-in sources such as patches, so their hashes are the same
+// in any checkout. Inputs in other repos can be generated during the fetch,
+// and inputs outside any repo are recorded as absolute paths.
+var localInputPrefixes = []string{
+	"FILE:@@//",
+	"DIRTREE:@@//",
+	"DIRENTS:@@//",
+}
+
+func isLocalInput(line string) bool {
+	for _, p := range localInputPrefixes {
+		if strings.HasPrefix(line, p) {
+			return true
+		}
+	}
+	return false
+}
+
 // readMarkerHash computes a hash from the stable lines of a marker file.
 // The first line is a hash of the repo rule's declarative inputs (URL,
 // version, patch paths) but does NOT include the content hashes of patch
 // files. Those appear on FILE: lines alongside their SHA-256 content
 // hashes. ENV: lines are skipped because environment variables can differ
 // between CI environments and would cause unnecessary hash instability.
+// Only inputs local to the main repo are hashed, see localInputPrefixes.
 func readMarkerHash(path string) ([]byte, error) {
 	f, err := os.Open(path)
 	if err != nil {
@@ -81,13 +105,16 @@ func readMarkerHash(path string) ([]byte, error) {
 
 	h := newHash()
 	hasContent := false
+	seenHeader := false
 	scanner := bufio.NewScanner(f)
 	for scanner.Scan() {
 		line := strings.TrimSpace(scanner.Text())
 		if line == "" {
 			continue
 		}
-		if strings.HasPrefix(line, "ENV:") {
+		isHeader := !seenHeader // first line: hash of the repo rule's declarative inputs
+		seenHeader = true
+		if !isHeader && !isLocalInput(line) {
 			continue
 		}
 		h.Write([]byte(line))
diff --git a/core/targethasher/markers_test.go b/core/targethasher/markers_test.go
new file mode 100644
index 00000000..e7b56cd9
--- /dev/null
+++ b/core/targethasher/markers_test.go
@@ -0,0 +1,118 @@
+// Copyright (c) 2026 Uber Technologies, Inc.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package targethasher
+
+import (
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+const (
+	testDigest     = "fbbfccf5194415fded38959668a5627efc0e02be1bbaa6420edf3c25c057b11a"
+	testPatchLine  = "FILE:@@//patches/protobuf/use_prebuilt_protoc.patch 0f4b98e755d6ad0cee62a8fe8ce36d02fe129936301a34fa59abe9bbd9945a43"
+	testGoEnvLine  = "FILE:@@gazelle++non_module_deps+bazel_gazelle_go_repository_cache//go.env 860dcdd7df8b260d298aa300fed108cda552d3e5420f2565fb742c3183025dbb"
+	testToolBinary = "FILE:@@gazelle++non_module_deps+bazel_gazelle_go_repository_tools//bin/gazelle 3c218b37322806fdfa4b7e6a090d7fd5db919b07df3dde930dc029c1854a9989"
+	testSourceFile = "FILE:@@gazelle+//BUILD.bazel eda52fca39edfb09f3c35adf12ad3bde86f4f92a7586b59eebfd3aea"
+	testMapping    = "REPO_MAPPING:gazelle+,bazel_tools bazel_tools"
+	testEnv        = "ENV:GOPATH /Users/someone/go-code"
+)
+
+func markerHash(t *testing.T, lines ...string) []byte {
+	t.Helper()
+	path := filepath.Join(t.TempDir(), "repo.marker")
+	require.NoError(t, os.WriteFile(path, []byte(strings.Join(lines, "\n")+"\n"), 0o644))
+	h, err := readMarkerHash(path)
+	require.NoError(t, err)
+	return h
+}
+
+func TestReadMarkerHash_IgnoresNonLocalAndEnvLines(t *testing.T) {
+	base := markerHash(t, testDigest, testPatchLine)
+
+	// Same digest and patch, but with every kind of line that must not count,
+	// including generated files whose hashes differ between workspaces.
+	withNoise := markerHash(t,
+		testDigest,
+		testGoEnvLine,
+		testToolBinary,
+		testSourceFile,
+		testPatchLine,
+		testMapping,
+		testEnv,
+	)
+	assert.Equal(t, base, withNoise)
+
+	otherWorkspace := markerHash(t,
+		testDigest,
+		strings.Replace(testGoEnvLine, "860dcdd7", "a0b4be1a", 1),
+		strings.Replace(testToolBinary, "3c218b37", "fcfe8347", 1),
+		testPatchLine,
+	)
+	assert.Equal(t, base, otherWorkspace, "path-dependent FILE: lines from other repos must not affect the hash")
+}
+
+func TestReadMarkerHash_ChangesOnRuleInputs(t *testing.T) {
+	base := markerHash(t, testDigest, testPatchLine)
+	bumped := markerHash(t, strings.Replace(testDigest, "fbbfccf5", "00000000", 1), testPatchLine)
+	assert.NotEqual(t, base, bumped, "first line (repo rule inputs) must affect the hash")
+}
+
+func TestReadMarkerHash_ChangesOnPatchContent(t *testing.T) {
+	base := markerHash(t, testDigest, testPatchLine)
+	edited := markerHash(t, testDigest, strings.Replace(testPatchLine, "0f4b98e7", "ffffffff", 1))
+	assert.NotEqual(t, base, edited, "main-repo FILE: lines (patches) must affect the hash")
+
+	added := markerHash(t, testDigest, testPatchLine, "FILE:@@//patches/protobuf/extra.patch 1111111111111111111111111111111111111111111111111111111111111111")
+	assert.NotEqual(t, base, added, "adding a patch must affect the hash")
+}
+
+func TestReadMarkerHash_LocalDirectoryInputs(t *testing.T) {
+	base := markerHash(t, testDigest, testPatchLine)
+
+	for _, kind := range []string{"DIRTREE", "DIRENTS"} {
+		local := kind + ":@@//patches/protobuf 1111111111111111111111111111111111111111111111111111111111111111"
+		withDir := markerHash(t, testDigest, testPatchLine, local)
+		assert.NotEqual(t, base, withDir, "main-repo %s: lines must affect the hash", kind)
+
+		changed := markerHash(t, testDigest, testPatchLine, strings.Replace(local, "11111111", "22222222", 1))
+		assert.NotEqual(t, withDir, changed, "main-repo %s: content must affect the hash", kind)
+
+		other := kind + ":@@gazelle+//cmd 1111111111111111111111111111111111111111111111111111111111111111"
+		assert.Equal(t, base, markerHash(t, testDigest, testPatchLine, other),
+			"%s: lines for other repos must not affect the hash", kind)
+	}
+}
+
+func TestReadMarkerHash_IgnoresAbsolutePathInputs(t *testing.T) {
+	base := markerHash(t, testDigest, testPatchLine)
+	// Inputs outside any repo are recorded as absolute paths, which are tied to
+	// the machine and not to the workspace's checked-in sources.
+	withAbsolute := markerHash(t, testDigest, testPatchLine,
+		"FILE:/usr/bin/env 1111111111111111111111111111111111111111111111111111111111111111")
+	assert.Equal(t, base, withAbsolute)
+}
+
+func TestReadMarkerHash_Empty(t *testing.T) {
+	path := filepath.Join(t.TempDir(), "empty.marker")
+	require.NoError(t, os.WriteFile(path, []byte("\n  \n"), 0o644))
+	h, err := readMarkerHash(path)
+	require.NoError(t, err)
+	assert.Nil(t, h)
+}