PokéBase - Pokémon Q&A
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It's mostly for the reason what JJ said, though I thought of some:

  • The ability Rivalry can be used on Heatran.
  • Some PokeBalls are based on the Pokemon's gender.

So yeah, any more abilities and stuff that requires gender is put to use.

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Thats what I was wondering, having a gender only makes him vulnerable to rivalry, attract, cute charm, and a few other moves, and Heatran's stats arent overwhelming so its not like its to balance him out. I cant think of any other dual gender pokemon who cant breed, it would have made more sense to make heatrans a single gender if they werent made genderless.
Nobody uses any of those things...
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It can't breed unfortunately. I'm not sure why it has a gender, maybe Game Freak just wanted to mix it up a bit.

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