PokéBase - Pokémon Q&A
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it does not make sense why they cannot mate

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I never even knew legendary`s had genders :D I learn something new every day

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Because even though they are opposite gender they are in the Undiscovered egg group. Pokemon in this Egg Group cant breed no matter what the circumstances.

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i get what youre saying but they are from the same species and that doesnt make sense why they cant mate
They can't breed because they are legendary Pokemon, and in the undiscovered egg group. Manaphy is the only one who breaks that rule. :P
Well Heatran, as a legendary pokemon, is both rare (there may not even be more than one, in-universe of course), and in all likelihood immortal. This would both make breeding difficult, but unnecessary. From Game Freak's perspective, they would not want trainers to have easy access to multiple, powerful legendary pokemon in the game and would want to make each individual legendary all the more special, and as such would not want legendaries to breed. Hope this helps
Well. That answers my question about the same thing I guess.
yeah thanks for your opinion
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Heat ran is in the undiscovered egg group, which the Pokemon are inbreed able. Gamefreak wanted legendaries to not breed, genders don't make a difference.

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Lol. another one of those "because GameFreak made it that way"