As noted by Daniel Huculak, you need to have cleared the first part of the game to unlock evolution. In post-game dungeons, evolution crystals can be found in Kecleon shops but are also guaranteed end-of-dungeon drops at the following dungeons (there may be others as well):
- Waterfall Pond (x2)
- Southern Cavern (x5)
- Buried Relic (x8)
- Marvelous Sea (x5)
Note that you don't actually need that many and since they can be found in many endgame shops, they are not particularly hard to get.
Note: Marvelous Sea and Buried Relic are not worth it if you're specifically trying to get Evolution Crystals - the former is unlocked very late and Buried Relic's drops are on the 99th floor. Southern Cavern can be incredibly challenging if you have just finished the first part of the story due to the prevalence of magnitude and earthquake by enemies and the length of the dungeon. For this reason, I recommend Waterfall Pond, though it is not a cakewalk either.