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I'm pretty sure Mewtwo was supposedly voiced by a BOY, making it look like one. However in the Genesect movie, Mewtwo was voice as a GIRL.

I get Mewtwo is genderless but it really confuses me.

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For starters, the two Mewtwos' are not the same entity.
Also, there's no clause which says "you must use the same voice actor for this character". They can do what they want (because they're 12).

Don't tell gender by the voice. Half the time male characters are voiced by female actresses, and sometimes the other way around.

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The original Mewtwo, created by team rocket (First Movie & Mewtwo Returns), was a male.
This is the moody Mewtwo you know best.

enter image description here

The second Mewtwo appears in Genesect and the Legend Awakened and is female.

There is no real evidence for exactly who created this Mewtwo, but it may have been another team following Giovanni's original plans. It could also have to do with the "multiple parallel universes" mentioned to exist in ORAS.

enter image description here
If this were to be the case, this Mewtwo would have been created at abut the same time in about the same circumstances, but was born a female and may have never met Ash.

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Sorry for the large image sizes, but I wanted the movie posters for reference.