diff --git a/src/palantir/plot.py b/src/palantir/plot.py
index 21c08eff..ed35d480 100644
--- a/src/palantir/plot.py
+++ b/src/palantir/plot.py
@@ -1940,7 +1940,9 @@ def plot_trajectory(
     arrowprops : dict, optional
         Properties for the arrowstyle. If None, defaults to black arrow with lw=1.
     scanpy_kwargs : dict, optional
-        Keyword arguments for the scanpy.pl.emebdding function to plot the cells.
+        Keyword arguments for the scanpy.pl.emebdding function to plot the cells
+        unless `masks_key == "branch_masks"` in which case these arguments are
+        passed to `matplotlib.pyplot.scatter`.
     figsize : Tuple[float, float], optional
         Size of the plot in inches, as (width, height). Defaults to (5, 5).
     **kwargs
@@ -1993,12 +1995,14 @@ def plot_trajectory(
             umap[~mask, 1],
             c=config.DESELECTED_COLOR,
             label="Other Cells",
+            **scanpy_kwargs
         )
         ax.scatter(
             umap[mask, 0],
             umap[mask, 1],
             c=config.SELECTED_COLOR,
             label="Selected Cells",
+            **scanpy_kwargs
         )
     elif cell_color is not None:
         b = embedding_basis[2:] if embedding_basis.startswith("X_") else embedding_basis