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At this time, there is no official compatibility list, and the emulator changes frequently enough that game compatibility changes faster than they can be tested. For the sake of visibility, below are a few links to compatibility lists that have been created by different people.
If a game is listed as being compatible with Citra but you are having trouble with it, please refer to the FAQ before posting to the support forum.
Nintendo 3DS Emulator Wiki
This link is only being provided for completion’s sake, but this list has not been updated in a long time and is very out of date.
Some games require some files to be dumped from a 3DS console and integrated into Citra in order to work. Below are known games requiring files. If you wish to play a game in one of the below lists, click the links for instructions on how to dump the necessary files from your 3DS console.
System Archives - Animal Crossing: New Leaf, Bravely Default, Bravely Second: End Layer, Kingdom Hearts: Dream Drop Distance, Kirby: Triple Deluxe, Luigi’s Mansion: Dark Moon, Mario Kart 7, Mario Party: Island Tour, Pokemon Alpha Sapphire, Pokemon Moon, Pokemon Omega Ruby, Pokemon Sun, Pokemon X, Pokemon Y, Super Mario 3D Land, Tomodachi Life