Hidden Shrines are one of the rare, hard to find items in Ghost of Tsushima. They are not listed in the collection tab, and they are not marked on the map either. The only clues are small wooden with a bowing figure on it. To bow, run your finger down the touchpad.
By performing this action in the right place, a small special effect will be triggered, like insects which will fly around you, birds appearing, fish jumping out of the water, and so on. Once 10 places have been honored, the trophy will unlock. There are more than 10 places to honor in total, but that does not add anything more to our knowledge.
You'll be free to come back to unlock these shrines once the story is over if you want.
Act 1 Hidden Shrines
Hidden Shrine 1: Near the duel place of the Tayadori Mythical Tale. Once activated, a whirlwind of flower petals will appear.
Hidden Shrine 2: In the cemetery not far from the forge. A black and red bird will appear on the right corner of the altar, high up.
Hidden Shrine 3: In Kechi Fishing Village, on the pontoon, by the water. Fish will jump everywhere.
Hidden Shrine 4: In front of a fox statue, next to a tree and a small pond, near a large house surrounded by red flowers. Firefly will swirl upon activation.
Hidden Shrine 5: At the end of the cemetery in the camp occupied by the Mongols, not far from where the leader was training. Butterflies will be circling around you.