This page on the Pokemon Ultra Sun and Ultra Moon Wiki Guide lists every difference between Ultra Sun and Ultra Moon, from exclusive Pokemon, to time differences, and more.

EditExclusive Pokemon

As it is with all other Pokemon titles, certain Pokemon will only appear in one version of the game and not the other.

EditExclusive Legendary Pokemon

All Legendary Pokemon (not Mythical!) are catchable in Pokemon Ultra Sun and Ultra Moon. However, some are only catchable in one version. These will be obtainable through Ultra Wormholes.

EditPokemon Ultra Sun Legendary Exclusives

EditPokemon Ultra Moon Legendary Exclusives

EditExlcusive Totem Sized Pokemon

Totem Pokemon are returning to Pokemon Ultra Sun and Ultra Moon, but this time, you’ll be able to add a few to your collection after finding special Totem Stickers. Here are the exclusives we know of so far.

Ultra Sun Exclusive		Ultra Moon Exclusive
Totem Sized Lurantis		Totem Sized Salazzle

EditUltra Recon Squad

The Ultra Recon Squad is a new team introduced in Pokemon Ultra Sun and Ultra Moon. In Ultra Sun, you’ll encounter Dulce and Zossie (left), but in Ultra Moon, you’ll encounter Phyco and Soliera (right).

EditTime Difference

Pokemon Ultra Sun and Ultra Moon will run 12 hours apart from each other, just like in Sun and Moon. If you’re playing Ultra Sun, the game will run in real time in accordance with your 3DS clock. If you’re playing Ultra Moon, the game will shift 12 hours from the 3DS clock.

This applies to almost the entire game, save for specific story scenes that take place at certain times of the day, no matter the game. So why is this important? There will be a few Pokemon the either only appear at either day or night, or their chances of appearing will differ depending on the time.

EditTotem Pokemon

Just like in Sun and Moon, some of the Totem Pokemon in Pokemon Ultra Sun and Ultra Moon will change depending on the version. For example, the Totem Pokemon encountered in Verdant Cavern on Melemele Island will be Gumshoos in Pokemon Ultra Sun, but the nocturnal Alolan Raticate in Pokemon Ultra Moon.