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Version-Exclusive Pokemon are Pokemon that is only found in the either version of the game. Those Pokemon couldn't be found and recruited in the dungeons until a Wonder Mail code involving the Pokemon is entered.

List of Pokemon Exclusive to PMD Red version

  • Porygon
  • Mantine
  • Plusle
  • Roselia
  • Feebas

Those Pokemon are absent from the Blue Version until a Wonder Mail code involving them is entered.

List of Pokemon Exclusive to the PMD Blue Version

  • Porygon2 (could be obtained in the Red Version by evolving Porygon)
  • Lapras
  • Minun
  • Aipom
  • Magikarp