diff --git a/src/anndata/_core/merge.py b/src/anndata/_core/merge.py
index 276db242f..1414bff98 100644
--- a/src/anndata/_core/merge.py
+++ b/src/anndata/_core/merge.py
@@ -189,6 +189,15 @@ def equal_sparse(a, b) -> bool:
             # Comparison broken for CSC matrices
             # https://github.com/cupy/cupy/issues/7757
             a, b = CupyCSRMatrix(a), CupyCSRMatrix(b)
+        if Version(scipy.__version__) >= Version("1.16.0rc1"):
+            # TODO: https://github.com/scipy/scipy/issues/23068
+            return bool(
+                a.format == b.format
+                and (a.shape == b.shape)
+                and np.all(a.indptr == b.indptr)
+                and np.all(a.indices == b.indices)
+                and np.all((a.data == b.data) | (np.isnan(a.data) & np.isnan(b.data)))
+            )
         comp = a != b
         if isinstance(comp, bool):
             return not comp