diff --git a/ChangeLog.md b/ChangeLog.md
index 38fa81a..235e225 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -2,6 +2,7 @@
 
 ## 2.0.1-dev (changes since 2.0.1 go here)
 
+ * Updated subsample function to be compatible with new version of pandas
  * A unified API for sourcetracking with Gibbs sampling, including
    leave-one-out cross-validation, has been created and is accessible as
    ``sourcetracker.gibbs``.
diff --git a/sourcetracker/_sourcetracker.py b/sourcetracker/_sourcetracker.py
index ed73ff3..894faee 100644
--- a/sourcetracker/_sourcetracker.py
+++ b/sourcetracker/_sourcetracker.py
@@ -231,8 +231,10 @@ def subsample_dataframe(df, depth, replace=False):
     pd.DataFrame
         Subsampled dataframe.
     '''
-    f = partial(subsample_counts, n=depth, replace=replace)
-    return df.apply(f, axis=1, reduce=False, raw=False)
+    def subsample(x):
+        return pd.Series(subsample_counts(x.values, n=depth, replace=replace),
+                         index=x.index)
+    return df.apply(subsample, axis=1)
 
 
 def generate_environment_assignments(n, num_sources):