The following Pokémon are unavailable in natural conditions during the Present Era history of the Mainline World:

• All Fossil Pokémon: Went functionally extinct at various points during the Ancient Eras. Unavailable at large during the Empty Eras, Previous Era and The Present Era up until around 3700, when fossil revivification projects obtain success.
  • This includes Fakémon fossil species such as the Achaqaiki line.
  • The exception is locked population clusters such as the one in the Tree of Beginning.
  • Except for Aerodactyl which was the first Fossil Pokémon released, the order of successful releases follows their Pokédex ordering.
  • Lileep is first made available ca. 3731 PE^{(~2 before Gen1)} , the first specimen given to Ravir Eisenhorth.
  • Anorith is first made available va. 3731 PE^{(~2 before Gen1)} , the first specimen given to Steven Stone.
• Voltorb line: Unavailable up until the Previous Era, when the first Pokéball concepts were created.
• Porygon line: Unavailable up until around 3720 when it is created.
• Castform: Unavailable up until around 3720 when it is created.
• Golett line: Unavailable up until the tail end of the Mainline Ancient Era when they are created. Available at large during the Previous Era and the Present Era, although their population is a theoretically fixed number.
• »Gyaōn (Pokémon): Went functionally extinct sometime during the Empty Eras. Unavailable in the Previous and Present Eras.
• Mewtwo: Unavailable up until 3732 PE^{(~1 before Gen1)} when it is created.
• Kyogre, Groudon and Rayquaza: Went functionally extinct at the end of the Mainline Ancient Era. Only the named specimens of the Warring Triad remain until the Present Era.
• Reshiram and Zekrom: Unavailable up until some point during the Ancient Era when they were spawned.
• Genesect Unavailable up until around 3740, when it is created. The baseline species would have existed up to some point during the Empty Eras.