diff --git a/src/application/ReferenceSourceImportEntries.ts b/src/application/ReferenceSourceImportEntries.ts
index 36dae99496..49c6f82f54 100644
--- a/src/application/ReferenceSourceImportEntries.ts
+++ b/src/application/ReferenceSourceImportEntries.ts
@@ -97,18 +97,22 @@ const resolveInternalSpecifier = (
   );
   if (logicalPathEscapesRoot(normalized))
     return { to: normalized, resolution: "unresolved" };
+  // Preserve directory intent before normalization removes terminal dot segments.
+  const directoryReference =
+    specifier.endsWith("/") || [".", ".."].includes(posix.basename(specifier));
   const suffixes = ["", ".ts", ".js", ".mjs", ".cjs", ".tsx", ".jsx"];
   const candidates = suffixes.flatMap((suffix) => [
-    `${normalized}${suffix}`,
-    `${normalized}/index${suffix}`,
+    ...(directoryReference ? [] : [`${normalized}${suffix}`]),
+    posix.join(normalized, `index${suffix}`),
   ]);
   // Retain present runtime files first; substitute only a missing counterpart.
   // Counterparts cover explicit filenames, not directory/index resolution.
-  candidates.push(
-    ...typescriptEmittedSourceCandidates(fromPath, normalized).map(
-      ({ path }) => path,
-    ),
-  );
+  if (!directoryReference)
+    candidates.push(
+      ...typescriptEmittedSourceCandidates(fromPath, normalized).map(
+        ({ path }) => path,
+      ),
+    );
   const match = lookupPath.resolveCandidates(candidates);
   return match === undefined
     ? { to: normalized, resolution: "unresolved" }
diff --git a/tests/boundary/cli/referenceSourceDirectoryImports.test.ts b/tests/boundary/cli/referenceSourceDirectoryImports.test.ts
new file mode 100644
index 0000000000..6270855cbc
--- /dev/null
+++ b/tests/boundary/cli/referenceSourceDirectoryImports.test.ts
@@ -0,0 +1,118 @@
+import { mkdir, writeFile } from "node:fs/promises";
+import { createRequire } from "node:module";
+import { dirname, join } from "node:path";
+
+import { describe, expect } from "vitest";
+
+import { historicalSourceGraphSchema } from "../../../src/domain/referenceSourceGraph.js";
+import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
+import { cliTest } from "../../support/cli/cliFixture.js";
+
+// Reference-source reads require no-follow opens; Windows reports unsupported.
+describe.skipIf(process.platform === "win32")(
+  "compiled reference-source directory imports",
+  () => {
+    cliTest(
+      "resolves directory spellings without selecting similarly named files",
+      async ({ cli }) => {
+        const workspace = await createTestTempDirectory(
+          "rea-reference-directory-imports-",
+        );
+        const root = join(workspace, "source");
+        const imports = [
+          ["slash.cjs", "./lib/", "lib/index.js"],
+          ["dot.cjs", "./lib/.", "lib/index.js"],
+          ["self.cjs", ".", "index.js"],
+          ["self-slash.cjs", "./", "index.js"],
+          ["nested/parent.cjs", "..", "index.js"],
+          ["nested/parent-slash.cjs", "../", "index.js"],
+          ["direct.cjs", "./lib.js", "lib.js"],
+          ["fallback.cjs", "./fallback", "fallback/index.js"],
+          ["legacy-order.cjs", "./dep", "dep/index.js"],
+        ] as const;
+        const unresolved = [
+          ["missing.cjs", "./missing/", "missing/"],
+          ["escape.cjs", "../outside/", "../outside/"],
+          ["main.ts", "./folder.js/.", "folder.js"],
+        ] as const;
+        const files = new Map<string, string>([
+          ["index.js", 'module.exports = "root index";\n'],
+          ["lib/index.js", 'module.exports = "library index";\n'],
+          ["lib.js", 'module.exports = "sibling JavaScript file";\n'],
+          ["lib.ts", 'export const value = "sibling TypeScript file";\n'],
+          ["fallback/index.js", 'module.exports = "fallback index";\n'],
+          ["dep/index.js", 'module.exports = "existing index priority";\n'],
+          ["dep.cjs", 'module.exports = "later CommonJS candidate";\n'],
+          [
+            "folder.ts",
+            'export const value = "emitted filename counterpart";\n',
+          ],
+          ["missing.js", 'module.exports = "not a directory";\n'],
+          ...[...imports, ...unresolved].map(
+            ([path, specifier]) =>
+              [path, `require(${JSON.stringify(specifier)});\n`] as const,
+          ),
+        ]);
+        await Promise.all(
+          [...files].map(async ([path, contents]) => {
+            const target = join(root, path);
+            await mkdir(dirname(target), { recursive: true });
+            await writeFile(target, contents);
+          }),
+        );
+        const outside = join(workspace, "outside", "index.js");
+        await mkdir(dirname(outside), { recursive: true });
+        await writeFile(outside, 'module.exports = "outside import root";\n');
+
+        // Node's loader establishes each fixture's meaning independently.
+        for (const [path, specifier, target] of imports)
+          expect(createRequire(join(root, path)).resolve(specifier)).toBe(
+            join(root, target),
+          );
+        expect(() =>
+          createRequire(join(root, "missing.cjs")).resolve("./missing/"),
+        ).toThrow();
+        expect(() =>
+          createRequire(join(root, "main.ts")).resolve("./folder.js/."),
+        ).toThrow();
+        expect(
+          createRequire(join(root, "escape.cjs")).resolve("../outside/"),
+        ).toBe(outside);
+
+        const result = await cli.run({
+          arguments: ["import-reference-source", root, "--json"],
+          environment: {
+            HOME: workspace,
+            XDG_CONFIG_HOME: workspace,
+            XDG_CACHE_HOME: workspace,
+          },
+        });
+        expect(result.exitCode).toBe(0);
+        const graph = historicalSourceGraphSchema.parse(result.json);
+        expect(graph.parse_failures).toEqual([]);
+        expect(graph.relationships).toHaveLength(
+          imports.length + unresolved.length,
+        );
+        for (const [from, , to] of imports)
+          expect.soft(graph.relationships, from).toContainEqual({
+            from_path: from,
+            to,
+            kind: "requires",
+            resolution: "internal",
+            parse_state: "parsed",
+          });
+        for (const [from, , to] of unresolved)
+          expect.soft(graph.relationships, from).toContainEqual({
+            from_path: from,
+            to,
+            kind: "requires",
+            resolution: "unresolved",
+            parse_state: "parsed",
+          });
+        expect(
+          graph.entries.some((entry) => entry.path.includes("outside")),
+        ).toBe(false);
+      },
+    );
+  },
+);