diff --git a/scripts/verify-conformance-fixtures.mjs b/scripts/verify-conformance-fixtures.mjs
index 7cf09addc0..2151a67db7 100644
--- a/scripts/verify-conformance-fixtures.mjs
+++ b/scripts/verify-conformance-fixtures.mjs
@@ -3,7 +3,11 @@ import { readFile } from "node:fs/promises";
 import { dirname, join, resolve } from "node:path";
 import { promisify } from "node:util";
 
-import { sha256 } from "./lib/conformance-fixtures.mjs";
+import {
+  generateLargeFixture,
+  sha256,
+  sourceDigest,
+} from "./lib/conformance-fixtures.mjs";
 
 const exec = promisify(execFile);
 const manifestPath = resolve(
@@ -16,6 +20,23 @@ const root = dirname(manifestPath);
 
 for (const fixture of manifest.fixtures) {
   const artifactPath = join(root, fixture.artifact);
+  const sources = [];
+  for (const source of fixture.sources ?? []) {
+    const content =
+      source.path === "generated/large.c"
+        ? generateLargeFixture()
+        : await readFile(join(process.cwd(), "tests/conformance", source.path));
+    if (sha256(content) !== source.sha256)
+      throw new Error(
+        `${fixture.name}: source hash mismatch for ${source.path}`,
+      );
+    sources.push({ path: source.path, content });
+  }
+  if (
+    fixture.sourceSha256 !== undefined &&
+    sourceDigest(sources) !== fixture.sourceSha256
+  )
+    throw new Error(`${fixture.name}: source manifest digest mismatch`);
   const artifact = await readFile(artifactPath);
   if (sha256(artifact) !== fixture.artifactSha256)
     throw new Error(`${fixture.name}: artifact hash mismatch`);
diff --git a/scripts/verify-real-hopper.mjs b/scripts/verify-real-hopper.mjs
index c45a79db80..51cd77f1f8 100644
--- a/scripts/verify-real-hopper.mjs
+++ b/scripts/verify-real-hopper.mjs
@@ -1,4 +1,6 @@
 import { execFile } from "node:child_process";
+import { createHash } from "node:crypto";
+import { createReadStream } from "node:fs";
 import { readdir, realpath } from "node:fs/promises";
 import { promisify } from "node:util";
 
@@ -8,6 +10,7 @@ import { StdioClientTransport } from "@modelcontextprotocol/client/stdio";
 import { TOOL_CONTRACTS } from "../dist/contracts/toolContracts.js";
 import {
   firstProcedureAddress,
+  requireDistinctTargetHashes,
   requireAddressArray,
   requireFunctionDossier,
   requirePseudocode,
@@ -253,6 +256,11 @@ const [targetA, targetB] = await Promise.all([
 ]);
 if (targetA === targetB)
   throw new Error("Real-Hopper verification requires two distinct targets");
+const [targetHashA, targetHashB] = await Promise.all([
+  sha256File(targetA),
+  sha256File(targetB),
+]);
+requireDistinctTargetHashes(targetHashA, targetHashB);
 const serverEnvironment = { ...process.env };
 delete serverEnvironment.HOPPER_TARGET_PATH;
 delete serverEnvironment.HOPPER_SECOND_TARGET_PATH;
@@ -377,6 +385,7 @@ try {
     diagnosticCount,
     dynamicSession: true,
     targets: [targetA, targetB],
+    targetHashes: [targetHashA, targetHashB],
     switched: true,
     secondOverview: verifiedSecondOverview,
   };
@@ -422,3 +431,9 @@ await new Promise((resolve, reject) => {
     },
   );
 });
+
+async function sha256File(path) {
+  const hash = createHash("sha256");
+  for await (const chunk of createReadStream(path)) hash.update(chunk);
+  return hash.digest("hex");
+}
diff --git a/src/application/RealHopperAssertions.ts b/src/application/RealHopperAssertions.ts
index 1e815f865d..45e12d22b1 100644
--- a/src/application/RealHopperAssertions.ts
+++ b/src/application/RealHopperAssertions.ts
@@ -27,6 +27,23 @@ export const firstProcedureAddress = (input: unknown): string => {
   return first.address;
 };
 
+/** Reject two target paths that resolve to the same binary content. */
+export const requireDistinctTargetHashes = (
+  firstHash: unknown,
+  secondHash: unknown,
+): void => {
+  if (
+    typeof firstHash !== "string" ||
+    typeof secondHash !== "string" ||
+    firstHash.length === 0 ||
+    secondHash.length === 0
+  ) {
+    throw new TypeError("Target hashes must be non-empty strings");
+  }
+  if (firstHash === secondHash)
+    throw new TypeError("Real-Hopper verification requires distinct binaries");
+};
+
 /** Reject empty and success-shaped embedded decompilation failures. */
 export const requirePseudocode = (
   input: unknown,
diff --git a/tests/realHopperAssertions.test.ts b/tests/realHopperAssertions.test.ts
index 0140ac591e..fe6d0424ed 100644
--- a/tests/realHopperAssertions.test.ts
+++ b/tests/realHopperAssertions.test.ts
@@ -2,12 +2,20 @@ import { describe, expect, it } from "vitest";
 
 import {
   firstProcedureAddress,
+  requireDistinctTargetHashes,
   requireAddressArray,
   requireFunctionDossier,
   requirePseudocode,
 } from "../src/application/RealHopperAssertions.js";
 
 describe("real Hopper semantic assertions", () => {
+  it("rejects two target paths containing the same binary", () => {
+    expect(() => requireDistinctTargetHashes("same", "same")).toThrow(
+      /distinct binaries/u,
+    );
+    expect(() => requireDistinctTargetHashes("", "other")).toThrow();
+    expect(() => requireDistinctTargetHashes("first", "second")).not.toThrow();
+  });
   it("extracts only a real procedure address from a structured page", () => {
     expect(
       firstProcedureAddress({