diff --git a/malariagen_data/anoph/fst.py b/malariagen_data/anoph/fst.py
index 7cd77d63a..e14b598db 100644
--- a/malariagen_data/anoph/fst.py
+++ b/malariagen_data/anoph/fst.py
@@ -1,3 +1,4 @@
+import warnings
 from typing import Tuple, Optional
 
 import numpy as np
@@ -81,6 +82,26 @@ def _fst_gwss(
                 chunks=chunks,
             ).compute()
 
+        n_snps = len(pos)
+        _min_snps_threshold = 1000
+        _window_adjustment_factor = 10
+        if n_snps < _min_snps_threshold:
+            raise ValueError(
+                f"Too few SNP sites ({n_snps}) available for Fst GWSS. "
+                f"At least {_min_snps_threshold} sites are required. "
+                "Try a larger genomic region or different site selection criteria."
+            )
+        if window_size >= n_snps:
+            adjusted_window_size = max(1, n_snps // _window_adjustment_factor)
+            warnings.warn(
+                f"window_size ({window_size}) is >= the number of SNP sites "
+                f"available ({n_snps}); automatically adjusting window_size to "
+                f"{adjusted_window_size} (= {n_snps} // {_window_adjustment_factor}).",
+                UserWarning,
+                stacklevel=2,
+            )
+            window_size = adjusted_window_size
+
         with self._spinner(desc="Compute Fst"):
             with np.errstate(divide="ignore", invalid="ignore"):
                 fst = allel.moving_hudson_fst(ac1, ac2, size=window_size)
@@ -96,7 +117,10 @@ def _fst_gwss(
     @doc(
         summary="""
             Run a Fst genome-wide scan to investigate genetic differentiation
-            between two cohorts.
+            between two cohorts. If window_size is >= the number of available
+            SNP sites, a UserWarning is issued and window_size is automatically
+            adjusted to number_of_snps // 10. A ValueError is raised if the
+            number of available SNP sites is below 1000.
         """,
         returns=dict(
             x="An array containing the window centre point genomic positions",
diff --git a/tests/anoph/test_fst.py b/tests/anoph/test_fst.py
index 790eb11b1..053e991fa 100644
--- a/tests/anoph/test_fst.py
+++ b/tests/anoph/test_fst.py
@@ -1,4 +1,5 @@
 import itertools
+import random
 import pytest
 from pytest_cases import parametrize_with_cases
 import numpy as np
@@ -139,6 +140,31 @@ def test_fst_gwss(fixture, api: AnophelesFstAnalysis):
     assert isinstance(fig, bokeh.models.GridPlot)
 
 
+@parametrize_with_cases("fixture,api", cases=".")
+def test_fst_gwss_window_size_too_large(fixture, api: AnophelesFstAnalysis):
+    # When window_size exceeds available SNPs, a UserWarning must be issued and
+    # the function must still return a valid result using the adjusted window_size.
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    all_countries = api.sample_metadata()["country"].dropna().unique().tolist()
+    countries = random.sample(all_countries, 2)
+    cohort1_query = f"country == {countries[0]!r}"
+    cohort2_query = f"country == {countries[1]!r}"
+    with pytest.warns(UserWarning, match="window_size"):
+        x, fst = api.fst_gwss(
+            contig=random.choice(api.contigs),
+            sample_sets=all_sample_sets,
+            cohort1_query=cohort1_query,
+            cohort2_query=cohort2_query,
+            site_mask=random.choice(api.site_mask_ids),
+            window_size=10_000_000,  # far larger than any fixture SNP count
+            min_cohort_size=1,
+        )
+    assert isinstance(x, np.ndarray)
+    assert isinstance(fst, np.ndarray)
+    assert len(x) > 0
+    assert x.shape == fst.shape
+
+
 @parametrize_with_cases("fixture,api", cases=".")
 def test_average_fst(fixture, api: AnophelesFstAnalysis):
     # Set up test parameters.