PokéBase - Pokémon Q&A
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If there are any. If Nintendo suggested people to come up with Pokémon ideas, I’m sure some pretty cool Pokémon would be made.

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There was a Pokemon called Marin, which was designed by a fan. It only appeared in the manga, though.

Marin (Japanese: マリン Marin) is a Pokémon appearing in the Magical Pokémon Journey manga. It appears only on the title page of The Best Gift Ever. According to commentary by Yumi Tsukirino, Marin was designed by a fan in a "draw Pikachu's friend" contest in Japan held by Ciao magazine (Japanese: ちゃお) and first published in the December 1998 issue of the same magazine in which the cover page is presented in color, and Marin's body is shown to be entirely blue.

Another instance of a fan-inspired Pokemon was when someone came up with an idea of a 'possessed' teacup on social media, which they named Polteageist.

Not an inspired design, but some fans speculated that in Ruby/Sapphire the character would be able to fly into space from the Mossdeep Space Centre and catch Deoxys. This was later found out to be false, but in OR/AS you can fly into space with Mega Rayquaza at the end of the Delta Episode and encounter a Deoxys.

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There has only been one official fan made Pokémon that has appeared in published media.

However, it was in the manga, which Game Freak does not publish. It was from a contest held in 1998 and the winner was the Pokémon, Marin

Source

Apparently, in 1998, a Japanese fan won a contest and their fan made Pokemon, Marin, was published in the Pokemon Adventures Manga.

This was the only example I could find! If an official Pokemon was actually fan-made, let me know!

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