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)

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

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Best answer

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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"I've been breeding for nine years"
Damn straight