diff --git a/.changeset/short-beds-run.md b/.changeset/short-beds-run.md
new file mode 100644
index 0000000000..3ee0199cc8
--- /dev/null
+++ b/.changeset/short-beds-run.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/resolve-dependencies": patch
+"pnpm": patch
+---
+
+Dedupe deps with the same alias in direct dependencies [6966](https://github.com/pnpm/pnpm/issues/6966)
diff --git a/pkg-manager/core/test/install/fromRepo.ts b/pkg-manager/core/test/install/fromRepo.ts
index 072cc9c501..b459c28e3e 100644
--- a/pkg-manager/core/test/install/fromRepo.ts
+++ b/pkg-manager/core/test/install/fromRepo.ts
@@ -233,3 +233,48 @@ test.skip('from a github repo that needs to be built. hoisted node linker is  us
   await install(manifest, await testDefaults({ frozenLockfile: true, ignoreScripts: true, nodeLinker: 'hoisted' }, { ignoreScripts: true }))
   await project.hasNot('@pnpm.e2e/prepare-script-works/prepare.txt')
 })
+
+test('re-adding a git repo with a different tag', async () => {
+  const project = prepareEmpty()
+  let manifest = await addDependenciesToPackage({}, ['kevva/is-negative#1.0.0'], await testDefaults())
+  await project.has('is-negative')
+  expect(manifest.dependencies).toStrictEqual({
+    'is-negative': 'github:kevva/is-negative#1.0.0',
+  })
+  expect(JSON.parse(fs.readFileSync('./node_modules/is-negative/package.json', 'utf8')).version).toBe('1.0.0')
+  let lockfile = await project.readLockfile()
+  expect(lockfile.dependencies['is-negative']).toEqual({
+    specifier: 'github:kevva/is-negative#1.0.0',
+    version: 'github.com/kevva/is-negative/163360a8d3ae6bee9524541043197ff356f8ed99',
+  })
+  expect(lockfile.packages).toEqual(
+    {
+      'github.com/kevva/is-negative/163360a8d3ae6bee9524541043197ff356f8ed99': {
+        resolution: { tarball: 'https://codeload.github.com/kevva/is-negative/tar.gz/163360a8d3ae6bee9524541043197ff356f8ed99' },
+        name: 'is-negative',
+        version: '1.0.0',
+        engines: { node: '>=0.10.0' },
+        dev: false,
+      },
+    }
+  )
+  manifest = await addDependenciesToPackage(manifest, ['kevva/is-negative#1.0.1'], await testDefaults())
+  await project.has('is-negative')
+  expect(JSON.parse(fs.readFileSync('./node_modules/is-negative/package.json', 'utf8')).version).toBe('1.0.1')
+  lockfile = await project.readLockfile()
+  expect(lockfile.dependencies['is-negative']).toEqual({
+    specifier: 'github:kevva/is-negative#1.0.1',
+    version: 'github.com/kevva/is-negative/9a89df745b2ec20ae7445d3d9853ceaeef5b0b72',
+  })
+  expect(lockfile.packages).toEqual(
+    {
+      'github.com/kevva/is-negative/9a89df745b2ec20ae7445d3d9853ceaeef5b0b72': {
+        resolution: { tarball: 'https://codeload.github.com/kevva/is-negative/tar.gz/9a89df745b2ec20ae7445d3d9853ceaeef5b0b72' },
+        name: 'is-negative',
+        version: '1.0.1',
+        engines: { node: '>=0.10.0' },
+        dev: false,
+      },
+    }
+  )
+})
diff --git a/pkg-manager/resolve-dependencies/src/resolveDependencyTree.ts b/pkg-manager/resolve-dependencies/src/resolveDependencyTree.ts
index acaeffe548..6c57dda9f4 100644
--- a/pkg-manager/resolve-dependencies/src/resolveDependencyTree.ts
+++ b/pkg-manager/resolve-dependencies/src/resolveDependencyTree.ts
@@ -187,10 +187,9 @@ export async function resolveDependencyTree<T> (
     }
   }
 
-  for (const { id } of importers) {
-    const directDeps = directDepsByImporterId[id]
+  for (const { id, wantedDependencies } of importers) {
+    const directDeps = dedupeSameAliasDirectDeps(directDepsByImporterId[id], wantedDependencies)
     const [linkedDependencies, directNonLinkedDeps] = partition((dep) => dep.isLinkedDependency === true, directDeps) as [LinkedDependency[], PkgAddress[]]
-
     resolvedImporters[id] = {
       directDependencies: directDeps
         .map((dep) => {
@@ -269,3 +268,28 @@ function buildTree (
   }
   return childrenNodeIds
 }
+
+/**
+  * There may be cases where multiple dependencies have the same alias in the directDeps array.
+  * E.g., when there is "is-negative: github:kevva/is-negative#1.0.0" in the package.json dependencies,
+  * and then re-execute `pnpm add github:kevva/is-negative#1.0.1`.
+  * In order to make sure that the latest 1.0.1 version is installed, we need to remove the duplicate dependency.
+  * fix https://github.com/pnpm/pnpm/issues/6966
+  */
+function dedupeSameAliasDirectDeps (directDeps: Array<PkgAddress | LinkedDependency>, wantedDependencies: Array<WantedDependency & { isNew?: boolean }>) {
+  const deps = new Map()
+  for (const directDep of directDeps) {
+    const { alias, normalizedPref } = directDep
+    if (!deps.has(alias)) {
+      deps.set(alias, directDep)
+    } else {
+      const wantedDep = wantedDependencies.find(dep =>
+        dep.alias ? dep.alias === alias : dep.pref === normalizedPref
+      )
+      if (wantedDep?.isNew) {
+        deps.set(alias, directDep)
+      }
+    }
+  }
+  return Array.from(deps.values())
+}