I have prepared this location guide to help you find the different runes scattered around the island in Sapphire Safari.
Mysterious Stone and Rune Locations
Here is Mysterious Stones and Rune locations in Sapphire Safari:
The Starting Location

The quest starts here!
Map location:

Hints
For those that don’t want the direct answer, each rune is located around the perimeter of the plains area, and they make a sparkly, ringing sound. Looking at night is recommended because they light up.
Rune Alpha

Rune Alpha is located in at the beginning of the map on the beach where the photo tutorial takes place.
Here’s a picture of the map:

and a picture of the physical location:

Rune Beta

Rune Beta is found in the swamp part of the map, in front of one of the nests, underneath one of the trees.
Here’s a picture of the map:

and a picture of the physical location:

Rune Gamma

Rune Gamma is found directly next to the mysterious rock in the desert where the runes are turned in.
Here’s a picture of the map:

and a picture of the physical location:

Rune Delta

Rune Delta is found at the top of the mountain located over the bridge in front of the plains base camp waterfall.
Here’s a picture of the map:

and the physical location:

Rune Epsilon

Rune Epsilon is located in the tall grass in the top left of the plains, across the chasm.
Here’s a picture of the map:

and a picture of the physical location:

How to Submit the Runes
- All runes must have their photos taken during the night cycle, when they are glowing.
- The photos must then be taken to the pillar in the desert and submitted.
- The developer has confirmed that the photos must be in your camera in order to turn them in.
- The runes can be submitted to the stone one at a time.