The Crystal Onix's first and only appearance is in the anime episode The Crystal Onix. Ash and his friends first heard of it through a note they found in a bottle floating in the ocean. The note was written by a little girl named Marissa. She wanted to find the Crystal Onix to help her brother, Mateo, gain inspiration to make glass Pokémon statues. Mateo told a story of how his grandfather discovered the Crystal Onix and then was able to make extraordinary sculptures afterwards. One of those sculptures included the Crystal Onix itself.
With the help of Marill, Tracey was able to assist greatly in finding the Crystal Onix's hideout.
The Crystal Onix in water
Besides being made of crystal, the Crystal Onix is also unique from other Onix in that it can live in water without being hurt by it. Its glass skin also gives it a special resistance to Template:Type2 attacks. Mateo realized that he would have to use a different type of attack to weaken it and so, he used his Charmeleon and attacked it with Fire Spin. It seemed to have a weakness to Template:Type2 attacks, unlike other Onix. Mateo was just about to capture it when he realized that he didn't need to. Just battling it gave him the inspiration he needed to create glass Pokémon sculptures. He thanked the Crystal Onix as it submerged itself into the water once more.