diff --git a/llvm/include/llvm/ProfileData/SampleProfReader.h b/llvm/include/llvm/ProfileData/SampleProfReader.h
--- a/llvm/include/llvm/ProfileData/SampleProfReader.h
+++ b/llvm/include/llvm/ProfileData/SampleProfReader.h
@@ -483,6 +483,9 @@
   /// Whether input profile contains ShouldBeInlined contexts.
   bool profileIsPreInlined() const { return ProfileIsPreInlined; }
 
+  /// Whether input profile is flow-sensitive.
+  bool profileIsFS() const { return ProfileIsFS; }
+
   virtual std::unique_ptr<ProfileSymbolList> getProfileSymbolList() {
     return nullptr;
   };
diff --git a/llvm/lib/CodeGen/MIRSampleProfile.cpp b/llvm/lib/CodeGen/MIRSampleProfile.cpp
--- a/llvm/lib/CodeGen/MIRSampleProfile.cpp
+++ b/llvm/lib/CodeGen/MIRSampleProfile.cpp
@@ -308,6 +308,15 @@
 }
 
 bool MIRProfileLoader::runOnFunction(MachineFunction &MF) {
+  // Do not load non-FS profiles. A line or probe can get a zero-valued
+  // discriminator at certain pass which could result in accidentally loading
+  // the corresponding base counter in the non-FS profile, while a non-zero
+  // discriminator would end up getting zero samples. This could in turn undo
+  // the sample distribution effort done by previous BFI maintenance and the
+  // probe distribution factor work for pseudo probes.
+  if (!Reader->profileIsFS())
+    return false;
+
   Function &Func = MF.getFunction();
   clearFunctionData(false);
   Samples = Reader->getSamplesFor(Func);
diff --git a/llvm/test/CodeGen/X86/fsafdo_test2.ll b/llvm/test/CodeGen/X86/fsafdo_test2.ll
--- a/llvm/test/CodeGen/X86/fsafdo_test2.ll
+++ b/llvm/test/CodeGen/X86/fsafdo_test2.ll
@@ -5,7 +5,8 @@
 ; RUN: llc -enable-fs-discriminator -improved-fs-discriminator=true < %s | FileCheck %s --check-prefixes=V1,V01
 ; RUN: llvm-profdata merge --sample -profile-isfs -o %t1.afdo %S/Inputs/fsloader_v1.afdo
 ; RUN: llc -enable-fs-discriminator -improved-fs-discriminator=true -fs-profile-file=%t1.afdo -show-fs-branchprob -disable-ra-fsprofile-loader=false -disable-layout-fsprofile-loader=false < %s 2>&1 | FileCheck %s --check-prefixes=LOADERV1,LOADER
-;
+; RUN: llc -enable-fs-discriminator -improved-fs-discriminator=true -fs-profile-file=%S/Inputs/fsloader_v1.afdo -profile-isfs -show-fs-branchprob -disable-ra-fsprofile-loader=false -disable-layout-fsprofile-loader=false < %s 2>&1 | FileCheck %s --check-prefixes=LOADERV1,LOADER
+; RUN: llc -enable-fs-discriminator -improved-fs-discriminator=true -fs-profile-file=%S/Inputs/fsloader_v1.afdo -show-fs-branchprob -disable-ra-fsprofile-loader=false -disable-layout-fsprofile-loader=false < %s 2>&1 | FileCheck %s --check-prefixes=NOLOAD
 ;;
 ;; C source code for the test (compiler at -O3):
 ;; // A test case for loop unroll.
@@ -82,6 +83,9 @@
 ; LOADER: Set branch fs prob: MBB (16 -> 18): unroll.c:24:11-->unroll.c:19:3 W=283590  0x30000000 / 0x80000000 = 37.50% --> 0x16588166 / 0x80000000 = 17.46%
 ; LOADER: Set branch fs prob: MBB (16 -> 17): unroll.c:24:11 W=283590  0x50000000 / 0x80000000 = 62.50% --> 0x69a77e9a / 0x80000000 = 82.54%
 
+;; Check that the profile is not loaded since the reader doesn't know it is a FS profile.
+; NOLOAD-NOT: Set branch fs prob
+
 target triple = "x86_64-unknown-linux-gnu"
 
 @sum = dso_local local_unnamed_addr global i32 0, align 4