PokéBase - Pokémon Q&A
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It just seems kind of odd.

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Junichi Masuda is the director of Game Freak, and he programmed the Masuda Method into the games so now it's called the Masuda Method as he is the creator if it.

I thought that it was Morimoto
Nope, Morimoto is also a Game Designer and Programmer, but he did not come up with and program the Masuda method. Shigeki Morimoto also designs pokemon, and he's best known for designing and creating Mew.