diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5060aa3..deeebf5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -109,3 +109,26 @@ jobs:
           vcfpartition --help
           python -m bio2zarr vcfpartition --help
 
+  test-numpy-version:
+    name: Test numpy versions
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        numpy: ["==1.26", ">=2"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install '.[dev]'
+      - name: Install numpy${{ matrix.numpy }}
+        run: |
+          python -m pip install 'numpy${{ matrix.numpy }}'
+      - name: Run tests
+        run: |
+          # We just run the CLI tests here because it doesn't require other upstream
+          # packages like sgkit (which are tangled up with the numpy 2 dependency)
+          python -m pytest tests/test_cli.py