diff --git a/python/tests/beagle_numba.py b/python/tests/beagle_numba.py
index 089dca0843..ee15681f06 100644
--- a/python/tests/beagle_numba.py
+++ b/python/tests/beagle_numba.py
@@ -457,8 +457,8 @@ def run_interpolation_beagle(
         stacklevel=1,
     )
     # Set marker indices.
-    typed_idx = np.where(query_h != -1)[0]
-    untyped_idx = np.where(query_h == -1)[0]
+    typed_idx = np.where(query_h != tskit.MISSING_DATA)[0]
+    untyped_idx = np.where(query_h == tskit.MISSING_DATA)[0]
     # Set physical positions of markers.
     typed_pos = pos[typed_idx]
     untyped_pos = pos[untyped_idx]
@@ -530,8 +530,8 @@ def run_tsimpute(
         stacklevel=1,
     )
     # Set markers indices.
-    typed_idx = np.where(query_h != -1)[0]
-    untyped_idx = np.where(query_h == -1)[0]
+    typed_idx = np.where(query_h != tskit.MISSING_DATA)[0]
+    untyped_idx = np.where(query_h == tskit.MISSING_DATA)[0]
     # Set physical positions of markers.
     typed_pos = pos[typed_idx]
     untyped_pos = pos[untyped_idx]