PokéBase - Pokémon Q&A
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I was wondering if the masuda method works on these Pokemon since their breeding is a little complicated.
For instance, if I breed a Volbeat and a foreign Ditto; it usually has a 50/50 chance of the Pokemon in the egg be a Volbeat or Illumise right? Technically those are two different Pokemon, so will the Masuda Method even work on them? Just curious. (This is for Pokemon XY btw)

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I'm pretty sure the Pokemon's species doesn't matter when determining shininess.

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Yes, it will work.
Whether or not the offspring is the same Pokemon as the non-Ditto parent you are using has no bearing on your chances of getting a shiny.
Although they are technically different species, in breeding mechanics they count simply as a male/female equivalent of the Pokemon you are breeding. It's not like you have less of a chance of getting a male shiny Charmander than a female if you used a Charizard to breed, for example.

Source: I've been breeding Pokemon for nine years.

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Thanks!
"I've been breeding for nine years"
~FlappersFlappers
Damn straight