diff --git a/libs/WindowManager/Shell/tests/flicker/src/com/android/wm/shell/flicker/apppairs/RotateTwoLaunchedAppsTransition.kt b/libs/WindowManager/Shell/tests/flicker/src/com/android/wm/shell/flicker/apppairs/RotateTwoLaunchedAppsTransition.kt
index 512fd9a58ea8b..277aca8fc01d2 100644
--- a/libs/WindowManager/Shell/tests/flicker/src/com/android/wm/shell/flicker/apppairs/RotateTwoLaunchedAppsTransition.kt
+++ b/libs/WindowManager/Shell/tests/flicker/src/com/android/wm/shell/flicker/apppairs/RotateTwoLaunchedAppsTransition.kt
@@ -22,7 +22,10 @@ import com.android.server.wm.flicker.FlickerTestParameter
 import com.android.server.wm.flicker.dsl.FlickerBuilder
 import com.android.server.wm.flicker.helpers.setRotation
 import com.android.server.wm.flicker.helpers.wakeUpAndGoToHomeScreen
+import com.android.wm.shell.flicker.helpers.BaseAppHelper.Companion.isShellTransitionsEnabled
 import com.android.wm.shell.flicker.helpers.SplitScreenHelper
+import org.junit.Assume.assumeFalse
+import org.junit.Before
 import org.junit.Test
 
 abstract class RotateTwoLaunchedAppsTransition(
@@ -52,6 +55,13 @@ abstract class RotateTwoLaunchedAppsTransition(
             }
         }
 
+    @Before
+    override fun setup() {
+        // AppPairs hasn't been updated to Shell Transition. There will be conflict on rotation.
+        assumeFalse(isShellTransitionsEnabled())
+        super.setup()
+    }
+
     @FlakyTest
     @Test
     override fun navBarLayerIsAlwaysVisible() {
diff --git a/libs/WindowManager/Shell/tests/flicker/src/com/android/wm/shell/flicker/helpers/BaseAppHelper.kt b/libs/WindowManager/Shell/tests/flicker/src/com/android/wm/shell/flicker/helpers/BaseAppHelper.kt
index 4fe69ad7fabe2..f15044ef37afa 100644
--- a/libs/WindowManager/Shell/tests/flicker/src/com/android/wm/shell/flicker/helpers/BaseAppHelper.kt
+++ b/libs/WindowManager/Shell/tests/flicker/src/com/android/wm/shell/flicker/helpers/BaseAppHelper.kt
@@ -20,6 +20,7 @@ import android.app.Instrumentation
 import android.content.ComponentName
 import android.content.pm.PackageManager.FEATURE_LEANBACK
 import android.content.pm.PackageManager.FEATURE_LEANBACK_ONLY
+import android.os.SystemProperties
 import android.support.test.launcherhelper.LauncherStrategyFactory
 import android.util.Log
 import androidx.test.uiautomator.By
@@ -60,6 +61,9 @@ abstract class BaseAppHelper(
     companion object {
         private const val APP_CLOSE_WAIT_TIME_MS = 3_000L
 
+        fun isShellTransitionsEnabled() =
+                SystemProperties.getBoolean("persist.debug.shell_transit", false)
+
         fun executeShellCommand(instrumentation: Instrumentation, cmd: String) {
             try {
                 SystemUtil.runShellCommand(instrumentation, cmd)
diff --git a/libs/WindowManager/Shell/tests/flicker/src/com/android/wm/shell/flicker/legacysplitscreen/LegacySplitScreenTransition.kt b/libs/WindowManager/Shell/tests/flicker/src/com/android/wm/shell/flicker/legacysplitscreen/LegacySplitScreenTransition.kt
index e8d4d1e9ada2e..16dfd853209ff 100644
--- a/libs/WindowManager/Shell/tests/flicker/src/com/android/wm/shell/flicker/legacysplitscreen/LegacySplitScreenTransition.kt
+++ b/libs/WindowManager/Shell/tests/flicker/src/com/android/wm/shell/flicker/legacysplitscreen/LegacySplitScreenTransition.kt
@@ -32,10 +32,12 @@ import com.android.server.wm.flicker.helpers.wakeUpAndGoToHomeScreen
 import com.android.server.wm.flicker.repetitions
 import com.android.server.wm.flicker.startRotation
 import com.android.server.wm.traces.parser.windowmanager.WindowManagerStateHelper
+import com.android.wm.shell.flicker.helpers.BaseAppHelper.Companion.isShellTransitionsEnabled
 import com.android.wm.shell.flicker.helpers.MultiWindowHelper.Companion.getDevEnableNonResizableMultiWindow
 import com.android.wm.shell.flicker.helpers.MultiWindowHelper.Companion.setDevEnableNonResizableMultiWindow
 import com.android.wm.shell.flicker.helpers.SplitScreenHelper
 import org.junit.After
+import org.junit.Assume.assumeFalse
 import org.junit.Before
 import org.junit.Test
 
@@ -52,6 +54,8 @@ abstract class LegacySplitScreenTransition(protected val testSpec: FlickerTestPa
 
     @Before
     open fun setup() {
+        // Legacy split is having some issue with Shell transition, and will be deprecated soon.
+        assumeFalse(isShellTransitionsEnabled())
         prevDevEnableNonResizableMultiWindow = getDevEnableNonResizableMultiWindow(context)
         if (prevDevEnableNonResizableMultiWindow != 0) {
             // Turn off the development option