diff --git a/app/src/GlobalStyles.tsx b/app/src/GlobalStyles.tsx
index 28acb1fd88..3c08ee7858 100644
--- a/app/src/GlobalStyles.tsx
+++ b/app/src/GlobalStyles.tsx
@@ -33,6 +33,8 @@ export function GlobalStyles() {
           --px-primary-color: #9efcfd;
           --px-primary-color--transparent: rgb(158, 252, 253, 0.2);
           --px-reference-color: #baa1f9;
+
+          --px-flex-gap-sm: ${theme.spacing.margin4}px;
         }
       `}
     />
diff --git a/app/src/components/canvas/PointCloud.tsx b/app/src/components/canvas/PointCloud.tsx
index b12c1c530f..7b7f8ce763 100644
--- a/app/src/components/canvas/PointCloud.tsx
+++ b/app/src/components/canvas/PointCloud.tsx
@@ -4,7 +4,6 @@ import { css } from "@emotion/react";
 import { theme } from "@arizeai/components";
 import {
   Axes,
-  ColorSchemes,
   getThreeDimensionalBounds,
   LassoSelect,
   ThreeDimensionalBounds,
@@ -16,6 +15,7 @@ import { usePointCloudStore } from "@phoenix/store";
 
 import { CanvasMode, CanvasModeRadioGroup } from "./CanvasModeRadioGroup";
 import { createColorFn } from "./coloring";
+import { DEFAULT_COLOR_SCHEME } from "./constants";
 import { ControlPanel } from "./ControlPanel";
 import { PointCloudClusters } from "./PointCloudClusters";
 import { PointCloudPoints } from "./PointCloudPoints";
@@ -37,7 +37,6 @@ interface ProjectionProps extends PointCloudProps {
 }
 
 const CONTROL_PANEL_WIDTH = 300;
-const DEFAULT_COLOR_SCHEME = ColorSchemes.Discrete2.WhiteLightBlue;
 /**
  * Displays the tools available on the point cloud
  * E.g. move vs select
diff --git a/app/src/components/canvas/PointCloudDisplaySettings.tsx b/app/src/components/canvas/PointCloudDisplaySettings.tsx
index b3db054ee4..2767822016 100644
--- a/app/src/components/canvas/PointCloudDisplaySettings.tsx
+++ b/app/src/components/canvas/PointCloudDisplaySettings.tsx
@@ -1,13 +1,19 @@
-import React from "react";
+import React, { ChangeEvent, useCallback, useMemo } from "react";
 import { css } from "@emotion/react";
 
 import { Form } from "@arizeai/components";
 
+import { useDatasets } from "@phoenix/contexts";
 import { usePointCloudStore } from "@phoenix/store";
+import { ColoringStrategy } from "@phoenix/types";
+import { assertUnreachable } from "@phoenix/typeUtils";
 
 import { ColoringStrategyPicker } from "./ColoringStrategyPicker";
+import { DEFAULT_COLOR_SCHEME, FALLBACK_COLOR } from "./constants";
+import { Shape, ShapeIcon } from "./ShapeIcon";
 
 export function PointCloudDisplaySettings() {
+  const { referenceDataset } = useDatasets();
   const [coloringStrategy, setColoringStrategy] = usePointCloudStore(
     (state) => [state.coloringStrategy, state.setColoringStrategy]
   );
@@ -25,6 +31,93 @@ export function PointCloudDisplaySettings() {
           onChange={setColoringStrategy}
         />
       </Form>
+      {}
+      {referenceDataset != null ? <DatasetVisibilitySettings /> : null}
     </section>
   );
+
+  function DatasetVisibilitySettings() {
+    const { datasetVisibility, setDatasetVisibility, coloringStrategy } =
+      usePointCloudStore((state) => ({
+        datasetVisibility: state.datasetVisibility,
+        setDatasetVisibility: state.setDatasetVisibility,
+        coloringStrategy: state.coloringStrategy,
+      }));
+
+    const handleDatasetVisibilityChange = useCallback(
+      (event: ChangeEvent) => {
+        const target = event.target as HTMLInputElement;
+        const { name, checked } = target;
+        setDatasetVisibility({
+          ...datasetVisibility,
+          [name]: checked,
+        });
+      },
+      [datasetVisibility, setDatasetVisibility]
+    );
+
+    const primaryColor = useMemo(() => {
+      switch (coloringStrategy) {
+        case ColoringStrategy.dataset:
+          return DEFAULT_COLOR_SCHEME[0];
+        case ColoringStrategy.correctness:
+          return FALLBACK_COLOR;
+        default:
+          assertUnreachable(coloringStrategy);
+      }
+    }, [coloringStrategy]);
+
+    const referenceColor = useMemo(() => {
+      switch (coloringStrategy) {
+        case ColoringStrategy.dataset:
+          return DEFAULT_COLOR_SCHEME[1];
+        case ColoringStrategy.correctness:
+          return FALLBACK_COLOR;
+        default:
+          assertUnreachable(coloringStrategy);
+      }
+    }, [coloringStrategy]);
+
+    const referenceShape =
+      coloringStrategy === ColoringStrategy.dataset
+        ? Shape.circle
+        : Shape.square;
+
+    return (
+      <form
+        css={css`
+          display: flex;
+          flex-direction: column;
+          gap: var(--px-flex-gap-sm);
+          label {
+            display: flex;
+            flex-direction: row;
+            gap: var(--px-flex-gap-sm);
+            align-items: center;
+          }
+        `}
+      >
+        <label>
+          <input
+            type="checkbox"
+            checked={datasetVisibility.primary}
+            name="primary"
+            onChange={handleDatasetVisibilityChange}
+          />
+          <ShapeIcon shape={Shape.circle} color={primaryColor} />
+          primary dataset
+        </label>
+        <label>
+          <input
+            type="checkbox"
+            checked={datasetVisibility.reference}
+            name="reference"
+            onChange={handleDatasetVisibilityChange}
+          />
+          <ShapeIcon shape={referenceShape} color={referenceColor} />
+          reference dataset
+        </label>
+      </form>
+    );
+  }
 }
diff --git a/app/src/components/canvas/PointCloudPoints.tsx b/app/src/components/canvas/PointCloudPoints.tsx
index 403c1defaf..0c099dfcb8 100644
--- a/app/src/components/canvas/PointCloudPoints.tsx
+++ b/app/src/components/canvas/PointCloudPoints.tsx
@@ -4,10 +4,19 @@ import { shade } from "polished";
 
 import { PointBaseProps, Points } from "@arizeai/point-cloud";
 
+import { usePointCloudStore } from "@phoenix/store";
+import { ColoringStrategy } from "@phoenix/types";
+
 import { PointColor, ThreeDimensionalPointItem } from "./types";
 
 const DIM_AMOUNT = 0.5;
 
+/**
+ * The amount to multiply the radius by to get the appropriate cube size
+ * E.g. size = radius * CUBE_RADIUS_MULTIPLIER
+ */
+const CUBE_RADIUS_MULTIPLIER = 1.7;
+
 /**
  * Invokes the color function if it is a function, otherwise returns the color
  * @param point
@@ -34,6 +43,11 @@ type PointCloudPointsProps = {
   selectedIds: Set<string>;
   radius: number;
 };
+
+/**
+ * Function component that renders the points in the point cloud
+ * Split out into it's own component to maximize performance and caching
+ */
 export function PointCloudPoints({
   primaryData,
   referenceData,
@@ -42,6 +56,21 @@ export function PointCloudPoints({
   referenceColor,
   radius,
 }: PointCloudPointsProps) {
+  const { datasetVisibility, coloringStrategy } = usePointCloudStore(
+    (state) => {
+      return {
+        datasetVisibility: state.datasetVisibility,
+        coloringStrategy: state.coloringStrategy,
+      };
+    }
+  );
+
+  // Only use a cube shape if the coloring strategy is not dataset
+  const referenceDatasetPointShape = useMemo(
+    () => (coloringStrategy !== ColoringStrategy.dataset ? "cube" : "sphere"),
+    [coloringStrategy]
+  );
+
   /** Colors to represent a dimmed variant of the color for "un-selected" */
   const dimmedPrimaryColor = useMemo<PointColor>(() => {
     if (typeof primaryColor === "function") {
@@ -77,18 +106,27 @@ export function PointCloudPoints({
     [referenceColor, selectedIds, dimmedReferenceColor]
   );
 
+  const showReferencePoints = datasetVisibility.reference && referenceData;
+
   return (
     <>
-      <Points
-        data={primaryData}
-        pointProps={{ color: primaryColorByFn, radius }}
-      />
-      {referenceData && (
+      {datasetVisibility.primary ? (
+        <Points
+          data={primaryData}
+          pointProps={{ color: primaryColorByFn, radius }}
+        />
+      ) : null}
+      {showReferencePoints ? (
         <Points
           data={referenceData}
-          pointProps={{ color: referenceColorByFn, radius }}
+          pointProps={{
+            color: referenceColorByFn,
+            radius,
+            size: radius ? radius * CUBE_RADIUS_MULTIPLIER : undefined,
+          }}
+          pointShape={referenceDatasetPointShape}
         />
-      )}
+      ) : null}
     </>
   );
 }
diff --git a/app/src/components/canvas/ShapeIcon.tsx b/app/src/components/canvas/ShapeIcon.tsx
new file mode 100644
index 0000000000..5daf9288b4
--- /dev/null
+++ b/app/src/components/canvas/ShapeIcon.tsx
@@ -0,0 +1,75 @@
+import React, { useMemo } from "react";
+import { css } from "@emotion/react";
+
+import { assertUnreachable } from "@phoenix/typeUtils";
+
+export enum Shape {
+  square = "square",
+  circle = "circle",
+}
+
+type ShapeIconProps = {
+  /**
+   * The shape of the icon / symbol
+   */
+  shape: Shape;
+  /**
+   * The color of the icon / symbol
+   */
+  color: string;
+};
+
+const SquareSVG = () => (
+  <svg
+    width="12px"
+    height="12px"
+    viewBox="0 0 12 12"
+    fill="none"
+    xmlns="http://www.w3.org/2000/svg"
+  >
+    <rect width="12" height="12" rx="1" fill="currentColor" />
+  </svg>
+);
+
+const CircleSVG = () => {
+  return (
+    <svg
+      width="12px"
+      height="12px"
+      viewBox="0 0 12 12"
+      fill="none"
+      xmlns="http://www.w3.org/2000/svg"
+    >
+      <circle cx="6" cy="6" r="6" fill="currentColor" />
+    </svg>
+  );
+};
+
+export function ShapeIcon(props: ShapeIconProps) {
+  const { shape, color } = props;
+  const shapeSVG = useMemo(() => {
+    switch (shape) {
+      case Shape.square:
+        return <SquareSVG />;
+      case Shape.circle:
+        return <CircleSVG />;
+      default:
+        assertUnreachable(shape);
+    }
+  }, [shape]);
+
+  return (
+    <i
+      className="shape-icon"
+      style={{ color }}
+      css={css`
+        display: flex;
+        flex-direction: row;
+        align-items: center;
+      `}
+      aria-hidden={true}
+    >
+      {shapeSVG}
+    </i>
+  );
+}
diff --git a/app/src/components/canvas/constants.ts b/app/src/components/canvas/constants.ts
new file mode 100644
index 0000000000..fc54bda243
--- /dev/null
+++ b/app/src/components/canvas/constants.ts
@@ -0,0 +1,8 @@
+import { ColorSchemes } from "@arizeai/point-cloud";
+
+export const DEFAULT_COLOR_SCHEME = ColorSchemes.Discrete2.WhiteLightBlue;
+
+/**
+ * The default color to use when coloringStrategy does not apply.
+ */
+export const FALLBACK_COLOR = "#555555";
diff --git a/app/src/store/pointCloudStore.ts b/app/src/store/pointCloudStore.ts
index 56e486c303..e27a8c16ca 100644
--- a/app/src/store/pointCloudStore.ts
+++ b/app/src/store/pointCloudStore.ts
@@ -3,6 +3,14 @@ import { devtools } from "zustand/middleware";
 
 import { ColoringStrategy } from "@phoenix/types";
 
+/**
+ * The visibility of the two datasets in the point cloud.
+ */
+type DatasetVisibility = {
+  primary: boolean;
+  reference: boolean;
+};
+
 export type PointCloudState = {
   /**
    * The IDs of the points that are currently selected.
@@ -28,6 +36,17 @@ export type PointCloudState = {
    * Sets the coloring strategy to the given value.
    */
   setColoringStrategy: (strategy: ColoringStrategy) => void;
+  /**
+   * The visibility of the two datasets in the point cloud.
+   * @default { primary: true, reference: true }
+   */
+  datasetVisibility: DatasetVisibility;
+  /**
+   * Sets the dataset visibility to the given value.
+   * @param {DatasetVisibility} visibility
+   * @returns {void}
+   */
+  setDatasetVisibility: (visibility: DatasetVisibility) => void;
 };
 
 const pointCloudStore: StateCreator<PointCloudState> = (set) => ({
@@ -37,6 +56,8 @@ const pointCloudStore: StateCreator<PointCloudState> = (set) => ({
   setSelectedClusterId: (id) => set({ selectedClusterId: id }),
   coloringStrategy: ColoringStrategy.dataset,
   setColoringStrategy: (strategy) => set({ coloringStrategy: strategy }),
+  datasetVisibility: { primary: true, reference: true },
+  setDatasetVisibility: (visibility) => set({ datasetVisibility: visibility }),
 });
 
 export const usePointCloudStore = create<PointCloudState>()(