diff --git a/lib/internal/assert/assertion_error.js b/lib/internal/assert/assertion_error.js
index 5dbf1e7a341380..788886c2c19524 100644
--- a/lib/internal/assert/assertion_error.js
+++ b/lib/internal/assert/assertion_error.js
@@ -182,6 +182,41 @@ function isSimpleDiff(actual, inspectedActual, expected, inspectedExpected) {
   return typeof actual !== 'object' || actual === null || typeof expected !== 'object' || expected === null;
 }
 
+// Produce a short, human-readable label for the prototype of `val` to be used
+// when surfacing prototype-mismatch information in the assertion diff. The
+// returned label is intentionally compact so that it can be appended to the
+// existing diff without overwhelming it.
+function describePrototype(val) {
+  const proto = ObjectGetPrototypeOf(val);
+  if (proto === null) {
+    return '[Object: null prototype]';
+  }
+  const ctor = proto.constructor;
+  if (typeof ctor === 'function' && typeof ctor.name === 'string' && ctor.name !== '') {
+    return ctor.name;
+  }
+  return '<anonymous>';
+}
+
+// Detect the case where two values inspect identically but are not
+// deep-strict-equal because their prototypes differ. In that situation the
+// usual diff is unhelpful (it shows the same text on both sides), so we want
+// to make the prototype mismatch explicit. Only top-level objects/functions
+// are considered; primitives reach this code path only when they trivially
+// fail simpler comparisons.
+function hasTopLevelPrototypeMismatch(actual, expected) {
+  if (actual === null || expected === null) {
+    return false;
+  }
+  const typeofActual = typeof actual;
+  const typeofExpected = typeof expected;
+  if ((typeofActual !== 'object' && typeofActual !== 'function') ||
+      (typeofExpected !== 'object' && typeofExpected !== 'function')) {
+    return false;
+  }
+  return ObjectGetPrototypeOf(actual) !== ObjectGetPrototypeOf(expected);
+}
+
 function createErrDiff(actual, expected, operator, customMessage, diffType = 'simple') {
   operator = checkOperator(actual, expected, operator);
 
@@ -204,15 +239,39 @@ function createErrDiff(actual, expected, operator, customMessage, diffType = 'si
       skipped = true;
     }
   } else if (inspectedActual === inspectedExpected) {
-    // Handles the case where the objects are structurally the same but different references
-    operator = 'notIdentical';
-    if (inspectedSplitActual.length > 50 && diffType !== 'full') {
-      message = `${ArrayPrototypeJoin(ArrayPrototypeSlice(inspectedSplitActual, 0, 50), '\n')}\n...}`;
-      skipped = true;
+    // The two values inspect identically. For deep-equality operators this
+    // typically means the prototypes differ in a way `inspect` cannot show
+    // (e.g. anonymous classes, or two distinct prototype objects with the
+    // same shape). Surface the prototype mismatch explicitly when present;
+    // otherwise fall back to the existing "not reference-equal" message,
+    // which covers e.g. `strictEqual([], [])`.
+    const prototypeMismatch = (operator === 'deepStrictEqual' ||
+                               operator === 'partialDeepStrictEqual') &&
+      hasTopLevelPrototypeMismatch(actual, expected);
+    if (prototypeMismatch) {
+      const actualProto = describePrototype(actual);
+      const expectedProto = describePrototype(expected);
+      const protoLine = `Object prototypes differ: ${actualProto} !== ${expectedProto}`;
+      let body;
+      if (inspectedSplitActual.length > 50 && diffType !== 'full') {
+        body = `${ArrayPrototypeJoin(ArrayPrototypeSlice(inspectedSplitActual, 0, 50), '\n')}\n...}`;
+        skipped = true;
+      } else {
+        body = ArrayPrototypeJoin(inspectedSplitActual, '\n');
+      }
+      message = `${protoLine}\n\n${body}`;
+      header = '';
     } else {
-      message = ArrayPrototypeJoin(inspectedSplitActual, '\n');
+      // Handles the case where the objects are structurally the same but different references
+      operator = 'notIdentical';
+      if (inspectedSplitActual.length > 50 && diffType !== 'full') {
+        message = `${ArrayPrototypeJoin(ArrayPrototypeSlice(inspectedSplitActual, 0, 50), '\n')}\n...}`;
+        skipped = true;
+      } else {
+        message = ArrayPrototypeJoin(inspectedSplitActual, '\n');
+      }
+      header = '';
     }
-    header = '';
   } else {
     const checkCommaDisparity = actual != null && typeof actual === 'object';
     const diff = myersDiff(inspectedSplitActual, inspectedSplitExpected, checkCommaDisparity);
diff --git a/test/parallel/test-assert-deep-prototype-diff.js b/test/parallel/test-assert-deep-prototype-diff.js
new file mode 100644
index 00000000000000..c3e64ce49dfdea
--- /dev/null
+++ b/test/parallel/test-assert-deep-prototype-diff.js
@@ -0,0 +1,115 @@
+'use strict';
+require('../common');
+const assert = require('assert');
+const { test } = require('node:test');
+
+// Disable colored output to prevent color codes from breaking assertion
+// message comparisons. This should only be an issue when process.stdout
+// is a TTY.
+if (process.stdout.isTTY) {
+  process.env.NODE_DISABLE_COLORS = '1';
+}
+
+// Regression tests for https://github.com/nodejs/node/issues/50397.
+//
+// When `assert.deepStrictEqual` fails solely because the two values have
+// different prototypes, the diff used to render as `{} !== {}` (or similar),
+// giving the user no clue about why the assertion failed. The assertion
+// error formatter now surfaces the prototype mismatch explicitly.
+
+test('deepStrictEqual surfaces anonymous-class prototype mismatch', () => {
+  const A = (() => class {})();
+  const B = (() => class {})();
+  assert.throws(
+    () => assert.deepStrictEqual(new A(), new B()),
+    (err) => {
+      assert.strictEqual(err.code, 'ERR_ASSERTION');
+      assert.match(err.message, /Object prototypes differ:/);
+      // The previous "Values have same structure but are not reference-equal"
+      // message must no longer be used for prototype-only mismatches because
+      // it is misleading: the values do not even have the same prototype.
+      assert.doesNotMatch(err.message, /same structure but are not reference-equal/);
+      return true;
+    }
+  );
+});
+
+test('deepStrictEqual surfaces named-class prototype mismatch', () => {
+  class Foo {}
+  class Bar {}
+  assert.throws(
+    () => assert.deepStrictEqual(new Foo(), new Bar()),
+    (err) => {
+      assert.strictEqual(err.code, 'ERR_ASSERTION');
+      // Both class names should appear somewhere in the rendered message:
+      // either in the existing inspect-based diff (`+ Foo {}` / `- Bar {}`)
+      // or in the new "Object prototypes differ:" line. The important
+      // guarantee is that the user can identify both prototypes from the
+      // error message alone.
+      assert.match(err.message, /Foo/);
+      assert.match(err.message, /Bar/);
+      return true;
+    }
+  );
+});
+
+test('deepStrictEqual surfaces null-prototype mismatch', () => {
+  const a = { __proto__: null };
+  const b = {};
+  assert.throws(
+    () => assert.deepStrictEqual(a, b),
+    (err) => {
+      assert.strictEqual(err.code, 'ERR_ASSERTION');
+      assert.match(err.message, /null prototype/);
+      return true;
+    }
+  );
+});
+
+test('deepStrictEqual prototype-mismatch message is helpful for empty objects', () => {
+  // This is the most pathological case: both sides inspect identically as
+  // `{}`, so without the prototype-mismatch information the diff body alone
+  // is useless. The fix must produce an explanatory line.
+  const A = (() => class {})();
+  const B = (() => class {})();
+  let captured;
+  try {
+    assert.deepStrictEqual(new A(), new B());
+  } catch (err) {
+    captured = err;
+  }
+  assert.ok(captured, 'deepStrictEqual should have thrown');
+  assert.match(captured.message, /Object prototypes differ:/);
+});
+
+test('strictEqual on structurally-equal arrays still uses notIdentical message', () => {
+  // Sanity check that the new code path does not regress the existing
+  // behavior of `strictEqual([], [])`. That comparison continues to use
+  // the "Values have same structure but are not reference-equal" message
+  // because the prototypes do match (both are Array.prototype).
+  assert.throws(
+    () => assert.strictEqual([], []),
+    {
+      code: 'ERR_ASSERTION',
+      message: 'Values have same structure but are not reference-equal:\n\n[]\n',
+    }
+  );
+});
+
+test('deepStrictEqual on structurally-equal values with same prototype still fails clearly', () => {
+  // When the prototypes match but the values are not reference-equal, the
+  // existing notIdentical fallback should still apply (deepStrictEqual on
+  // two equal-shape objects with the same prototype should normally pass;
+  // here we use objects whose enumerable properties differ to exercise the
+  // ordinary diff path and confirm it is unaffected).
+  assert.throws(
+    () => assert.deepStrictEqual({ a: 1 }, { a: 2 }),
+    (err) => {
+      assert.strictEqual(err.code, 'ERR_ASSERTION');
+      // The ordinary diff path must NOT mention prototype differences
+      // because the prototypes are identical.
+      assert.doesNotMatch(err.message, /Object prototypes differ:/);
+      return true;
+    }
+  );
+});