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strong evidence for pokemon having genitals:
organic pokemon have genders, while inorganic ones don't. if their gender was a more abstract quality then any of them could have genders.
pokemon have been seen to have buttholes. especially in torchic this would be the same orifice as used for standard bird reproduction.
flower pokemon or pokemon with flowers such as venusaur may be seen with differences to their flowers. particularly differences in the core of them are actual visible confirmed male and female genitals. if it's true for their plant components it's likely also true for their animal components. (plant pokemon, at least ones which are not also part animal, possibly only have genitals in the form of their flowers)
