diff --git a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/activities/EmulationActivity.java b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/activities/EmulationActivity.java
index 7ac735e7d9..7aa2800ea4 100644
--- a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/activities/EmulationActivity.java
+++ b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/activities/EmulationActivity.java
@@ -2,13 +2,17 @@ package org.dolphinemu.dolphinemu.activities;
 
 import android.app.Activity;
 import android.app.ActivityOptions;
+import android.app.AlertDialog;
 import android.app.Fragment;
 import android.content.Context;
+import android.content.DialogInterface;
 import android.content.Intent;
+import android.content.SharedPreferences;
 import android.hardware.usb.UsbManager;
 import android.os.Bundle;
 import android.os.Handler;
 import android.os.Message;
+import android.preference.PreferenceManager;
 import android.support.v7.app.AppCompatActivity;
 import android.view.InputDevice;
 import android.view.KeyEvent;
@@ -48,6 +52,8 @@ public final class EmulationActivity extends AppCompatActivity
 
 	private String mSubmenuFragmentTag;
 
+	private SharedPreferences mPreferences;
+
 	// So that MainActivity knows which view to invalidate before the return animation.
 	private int mPosition;
 
@@ -212,6 +218,8 @@ public final class EmulationActivity extends AppCompatActivity
 			}
 		}
 
+		mPreferences = PreferenceManager.getDefaultSharedPreferences(this);
+
 		mIsGameCubeGame = (NativeLibrary.GetPlatform(path) == 0);
 	}
 
@@ -387,13 +395,92 @@ public final class EmulationActivity extends AppCompatActivity
 	{
 		switch (id)
 		{
-			// Enable/Disable input overlay.
+			// Enable/Disable specific buttons or the entire input overlay.
 			case R.id.menu_emulation_input_overlay:
 			{
-				EmulationFragment emulationFragment = (EmulationFragment) getFragmentManager()
-						.findFragmentByTag(EmulationFragment.FRAGMENT_TAG);
+				boolean[] enabledButtons = new boolean[11];
+				AlertDialog.Builder builder = new AlertDialog.Builder(this);
+				builder.setTitle(R.string.emulation_toggle_input);
+				if (mIsGameCubeGame)
+				{
+					for (int i = 0; i < enabledButtons.length; i++)
+					{
+						enabledButtons[i] = mPreferences.getBoolean("buttonToggleGc" + i, true);
+					}
+					builder.setMultiChoiceItems(R.array.gcpadButtons, enabledButtons,
+							new DialogInterface.OnMultiChoiceClickListener()
+					{
+						@Override
+						public void onClick(DialogInterface dialog, int indexSelected, boolean isChecked)
+						{
+							SharedPreferences.Editor editor = mPreferences.edit();
 
-				emulationFragment.toggleInputOverlayVisibility();
+							if (mPreferences.getBoolean("buttonToggleGc" + indexSelected, true))
+							{
+								// If the button is enabled, disable it.
+								editor.putBoolean("buttonToggleGc" + indexSelected, false);
+							}
+							else
+							{
+								// If the button is disabled, enable it.
+								editor.putBoolean("buttonToggleGc" + indexSelected, true);
+							}
+							editor.apply();
+						}
+					});
+				}
+				else
+				{
+					for (int i = 0; i < enabledButtons.length; i++)
+					{
+						enabledButtons[i] = mPreferences.getBoolean("buttonToggleWii" + i, true);
+					}
+					builder.setMultiChoiceItems(R.array.wiimoteButtons, enabledButtons,
+							new DialogInterface.OnMultiChoiceClickListener()
+					{
+						@Override
+						public void onClick(DialogInterface dialog, int indexSelected, boolean isChecked)
+						{
+							SharedPreferences.Editor editor = mPreferences.edit();
+
+							if (mPreferences.getBoolean("buttonToggleWii" + indexSelected, true))
+							{
+								// If the button is enabled, disable it.
+								editor.putBoolean("buttonToggleWii" + indexSelected, false);
+							}
+							else
+							{
+								// If the button is disabled, enable it.
+								editor.putBoolean("buttonToggleWii" + indexSelected, true);
+							}
+
+							editor.apply();
+						}
+					});
+				}
+				builder.setNeutralButton(getString(R.string.emulation_toggle_all), new DialogInterface.OnClickListener()
+				{
+					@Override
+					public void onClick(DialogInterface dialogInterface, int i)
+					{
+						EmulationFragment emulationFragment = (EmulationFragment) getFragmentManager()
+								.findFragmentByTag(EmulationFragment.FRAGMENT_TAG);
+						emulationFragment.toggleInputOverlayVisibility();
+					}
+				});
+				builder.setPositiveButton(getString(R.string.emulation_done), new DialogInterface.OnClickListener()
+				{
+					@Override
+					public void onClick(DialogInterface dialogInterface, int i)
+					{
+						EmulationFragment emulationFragment = (EmulationFragment) getFragmentManager()
+								.findFragmentByTag(EmulationFragment.FRAGMENT_TAG);
+						emulationFragment.refreshInputOverlay();
+					}
+				});
+
+				AlertDialog alertDialog = builder.create();
+				alertDialog.show();
 
 				return;
 			}
diff --git a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/fragments/EmulationFragment.java b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/fragments/EmulationFragment.java
index 56a8b60c46..b70196a773 100644
--- a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/fragments/EmulationFragment.java
+++ b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/fragments/EmulationFragment.java
@@ -162,6 +162,11 @@ public final class EmulationFragment extends Fragment implements SurfaceHolder.C
 		editor.apply();
 	}
 
+	public void refreshInputOverlay()
+	{
+		mInputOverlay.refreshControls();
+	}
+
 	@Override
 	public void surfaceCreated(SurfaceHolder holder)
 	{
diff --git a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/overlay/InputOverlay.java b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/overlay/InputOverlay.java
index b37343d128..cbdcc57246 100644
--- a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/overlay/InputOverlay.java
+++ b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/overlay/InputOverlay.java
@@ -46,6 +46,8 @@ public final class InputOverlay extends SurfaceView implements OnTouchListener
 	private InputOverlayDrawableDpad mDpadBeingConfigured;
 	private InputOverlayDrawableJoystick mJoystickBeingConfigured;
 
+	private SharedPreferences mPreferences;
+
 	/**
 	 * Resizes a {@link Bitmap} by a given scale factor
 	 * 
@@ -78,47 +80,10 @@ public final class InputOverlay extends SurfaceView implements OnTouchListener
 	{
 		super(context, attrs);
 
-		// Add all the overlay items to the HashSet.
-		if (EmulationActivity.isGameCubeGame())
-		{
-			// GameCube
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.gcpad_a, ButtonType.BUTTON_A));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.gcpad_b, ButtonType.BUTTON_B));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.gcpad_x, ButtonType.BUTTON_X));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.gcpad_y, ButtonType.BUTTON_Y));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.gcpad_z, ButtonType.BUTTON_Z));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.gcpad_start, ButtonType.BUTTON_START));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.gcpad_l, ButtonType.TRIGGER_L));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.gcpad_r, ButtonType.TRIGGER_R));
-			overlayDpads.add(initializeOverlayDpad(context, R.drawable.gcwii_dpad,
-					ButtonType.BUTTON_UP, ButtonType.BUTTON_DOWN,
-					ButtonType.BUTTON_LEFT, ButtonType.BUTTON_RIGHT));
-			overlayJoysticks.add(initializeOverlayJoystick(context,
-					R.drawable.gcwii_joystick_range, R.drawable.gcwii_joystick,
-					ButtonType.STICK_MAIN));
-			overlayJoysticks.add(initializeOverlayJoystick(context,
-					R.drawable.gcwii_joystick_range, R.drawable.gcpad_c,
-					ButtonType.STICK_C));
-		}
-		else
-		{
-			// Wiimote + Nunchuk
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.wiimote_a, ButtonType.WIIMOTE_BUTTON_A));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.wiimote_b, ButtonType.WIIMOTE_BUTTON_B));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.wiimote_one, ButtonType.WIIMOTE_BUTTON_1));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.wiimote_two, ButtonType.WIIMOTE_BUTTON_2));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.wiimote_plus, ButtonType.WIIMOTE_BUTTON_PLUS));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.wiimote_minus, ButtonType.WIIMOTE_BUTTON_MINUS));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.wiimote_home, ButtonType.WIIMOTE_BUTTON_HOME));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.nunchuk_c, ButtonType.NUNCHUK_BUTTON_C));
-			overlayButtons.add(initializeOverlayButton(context, R.drawable.nunchuk_z, ButtonType.NUNCHUK_BUTTON_Z));
-			overlayDpads.add(initializeOverlayDpad(context, R.drawable.gcwii_dpad,
-					ButtonType.WIIMOTE_UP, ButtonType.WIIMOTE_DOWN,
-					ButtonType.WIIMOTE_LEFT, ButtonType.WIIMOTE_RIGHT));
-			overlayJoysticks.add(initializeOverlayJoystick(context,
-					R.drawable.gcwii_joystick_range, R.drawable.gcwii_joystick,
-					ButtonType.NUNCHUK_STICK));
-		}
+		mPreferences = PreferenceManager.getDefaultSharedPreferences(getContext());
+
+		// Load the controls.
+		refreshControls();
 
 		// Set the on touch listener.
 		setOnTouchListener(this);
@@ -358,6 +323,124 @@ public final class InputOverlay extends SurfaceView implements OnTouchListener
 		return true;
 	}
 
+	public void refreshControls()
+	{
+		// Remove all the overlay buttons from the HashSet.
+		overlayButtons.removeAll(overlayButtons);
+		overlayDpads.removeAll(overlayDpads);
+		overlayJoysticks.removeAll(overlayJoysticks);
+
+		// Add all the enabled overlay items back to the HashSet.
+		if (EmulationActivity.isGameCubeGame())
+		{
+			// GameCube
+			if (mPreferences.getBoolean("buttonToggleGc0", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.gcpad_a, ButtonType.BUTTON_A));
+			}
+			if (mPreferences.getBoolean("buttonToggleGc1", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.gcpad_b, ButtonType.BUTTON_B));
+			}
+			if (mPreferences.getBoolean("buttonToggleGc2", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.gcpad_x, ButtonType.BUTTON_X));
+			}
+			if (mPreferences.getBoolean("buttonToggleGc3", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.gcpad_y, ButtonType.BUTTON_Y));
+			}
+			if (mPreferences.getBoolean("buttonToggleGc4", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.gcpad_z, ButtonType.BUTTON_Z));
+			}
+			if (mPreferences.getBoolean("buttonToggleGc5", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.gcpad_start, ButtonType.BUTTON_START));
+			}
+			if (mPreferences.getBoolean("buttonToggleGc6", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.gcpad_l, ButtonType.TRIGGER_L));
+			}
+			if (mPreferences.getBoolean("buttonToggleGc7", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.gcpad_r, ButtonType.TRIGGER_R));
+			}
+			if (mPreferences.getBoolean("buttonToggleGc8", true))
+			{
+				overlayDpads.add(initializeOverlayDpad(getContext(), R.drawable.gcwii_dpad,
+						ButtonType.BUTTON_UP, ButtonType.BUTTON_DOWN,
+						ButtonType.BUTTON_LEFT, ButtonType.BUTTON_RIGHT));
+			}
+			if (mPreferences.getBoolean("buttonToggleGc9", true))
+			{
+				overlayJoysticks.add(initializeOverlayJoystick(getContext(),
+						R.drawable.gcwii_joystick_range, R.drawable.gcwii_joystick,
+						ButtonType.STICK_MAIN));
+			}
+			if (mPreferences.getBoolean("buttonToggleGc10", true))
+			{
+				overlayJoysticks.add(initializeOverlayJoystick(getContext(),
+						R.drawable.gcwii_joystick_range, R.drawable.gcpad_c,
+						ButtonType.STICK_C));
+			}
+		}
+		else
+		{
+			// Wiimote + Nunchuk
+			if (mPreferences.getBoolean("buttonToggleWii0", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.wiimote_a, ButtonType.WIIMOTE_BUTTON_A));
+			}
+			if (mPreferences.getBoolean("buttonToggleWii1", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.wiimote_b, ButtonType.WIIMOTE_BUTTON_B));
+			}
+			if (mPreferences.getBoolean("buttonToggleWii2", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.wiimote_one, ButtonType.WIIMOTE_BUTTON_1));
+			}
+			if (mPreferences.getBoolean("buttonToggleWii3", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.wiimote_two, ButtonType.WIIMOTE_BUTTON_2));
+			}
+			if (mPreferences.getBoolean("buttonToggleWii4", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.wiimote_plus, ButtonType.WIIMOTE_BUTTON_PLUS));
+			}
+			if (mPreferences.getBoolean("buttonToggleWii5", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.wiimote_minus, ButtonType.WIIMOTE_BUTTON_MINUS));
+			}
+			if (mPreferences.getBoolean("buttonToggleWii6", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.wiimote_home, ButtonType.WIIMOTE_BUTTON_HOME));
+			}
+			if (mPreferences.getBoolean("buttonToggleWii7", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.nunchuk_c, ButtonType.NUNCHUK_BUTTON_C));
+			}
+			if (mPreferences.getBoolean("buttonToggleWii8", true))
+			{
+				overlayButtons.add(initializeOverlayButton(getContext(), R.drawable.nunchuk_z, ButtonType.NUNCHUK_BUTTON_Z));
+			}
+			if (mPreferences.getBoolean("buttonToggleWii9", true))
+			{
+				overlayDpads.add(initializeOverlayDpad(getContext(), R.drawable.gcwii_dpad,
+						ButtonType.WIIMOTE_UP, ButtonType.WIIMOTE_DOWN,
+						ButtonType.WIIMOTE_LEFT, ButtonType.WIIMOTE_RIGHT));
+			}
+			if (mPreferences.getBoolean("buttonToggleWii10", true))
+			{
+				overlayJoysticks.add(initializeOverlayJoystick(getContext(),
+						R.drawable.gcwii_joystick_range, R.drawable.gcwii_joystick,
+						ButtonType.NUNCHUK_STICK));
+			}
+		}
+
+		invalidate();
+	}
+
 	private void saveControlPosition(int sharedPrefsId, int x, int y)
 	{
 		final SharedPreferences sPrefs = PreferenceManager.getDefaultSharedPreferences(getContext());
diff --git a/Source/Android/app/src/main/res/values/arrays.xml b/Source/Android/app/src/main/res/values/arrays.xml
index 4335648861..62a15789d2 100644
--- a/Source/Android/app/src/main/res/values/arrays.xml
+++ b/Source/Android/app/src/main/res/values/arrays.xml
@@ -159,6 +159,20 @@
         <item>12</item>
     </integer-array>
 
+    <string-array name="gcpadButtons">
+        <item>A</item>
+        <item>B</item>
+        <item>X</item>
+        <item>Y</item>
+        <item>Z</item>
+        <item>Start</item>
+        <item>L</item>
+        <item>R</item>
+        <item>D-Pad</item>
+        <item>Main Stick</item>
+        <item>C Stick</item>
+    </string-array>
+
     <string-array name="wiimoteTypeEntries">
         <item>Disabled</item>
         <item>Emulated</item>
@@ -170,4 +184,18 @@
         <item>2</item>
     </integer-array>
 
+    <string-array name="wiimoteButtons">
+        <item>A</item>
+        <item>B</item>
+        <item>1</item>
+        <item>2</item>
+        <item>+</item>
+        <item>-</item>
+	<item>Home</item>
+        <item>C</item>
+        <item>Z</item>
+        <item>D-Pad</item>
+        <item>Nunchuk Stick</item>
+    </string-array>
+
 </resources>
diff --git a/Source/Android/app/src/main/res/values/strings.xml b/Source/Android/app/src/main/res/values/strings.xml
index 04db68eee8..5ad4e029b3 100644
--- a/Source/Android/app/src/main/res/values/strings.xml
+++ b/Source/Android/app/src/main/res/values/strings.xml
@@ -356,6 +356,7 @@
 
     <!-- Emulation Menu -->
     <string name="emulation_toggle_input">Toggle Touch Controls</string>
+    <string name="emulation_toggle_all">Toggle All</string>
     <string name="emulation_quicksave">Quick Save</string>
     <string name="emulation_quickload">Quick Load</string>
     <string name="emulation_refresh_wiimotes">Refresh Wiimotes</string>