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Porygon 2, Porygon-Z, Serperior, Emboar, Samurott, Stoutland, Purrloin, Liepard, Simisage, Simipour, Unfezant, Boldore, Gigalith, Gurdurr, Conkeldurr, Seismitoad, Throh, Sawk, Whimsicott, Petilil, Lilligant, Krookodile, Maractus, Crustle, Sigilyph, Tirtouga, Carracosta, Garbodor, Cinccino, Gothorita, Duosion, Reuniclus, Vanillish, Vanilluxe, Karrablast, Amoonguss, Jellicent, Ferroseed, Ferrothorn, Klink, Klang, Klinklang, Eelektrik, Cryogonal, Shelmet, Accelgor, Mienfoo, Mienshao, Pawniard, Bisharp, Rufflet, Braviary, Vullaby, Mandibuzz, Heatmor, Durant, Deino, Zweilous, Hydreigon, Larvesta, Volcarona, Cobalion, Terrakion, Virizion, Tornadus, Thundurus, Reshiram, Landorus, Kyurem, Keldeo, Meloetta, and Genesect, all have never been seen in the anime yet.

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Actually, a few of those have appeared in anime, and a few in the movie, too.
Desmond remember this was from 6 months ago there have been more episodes in the last 6 months
Simipour emboar Samurott Stoutland Purrloin unfezat Throh Swak Lilligant Maractus heatmor Reuniclus Durant Tronadus Thunduruns Landorus Reshiram Bisharp Shelmet Accelgor Mienfoo Mienshao Larvesta  Gothorita Gigalith Carracosta Purrloin  have been seen in the anime.
Reshiram is in a MOVIE
Reshiram's movie came out after this answer. =-= No need to be rude with your caps.
actually, in the most RECENT episode, Ash FINALLY defeated Trip's Serperior, thanks to an Electro-Ball-Iron-Tail combo. Man, it was sweet. the look on Trip's FACE sent me laughing. He was in total shock. I don't think Trip expected to be defeated by an ELECTRIC type. What amazes me is that Trip and Ash actually shook hands in the Pokemon Center. I was like "WHAT THE...?". I was, and still am, confused by that little hand-shake.
wait, maractus?? i thought cilan had one
@ cheren2345: What does that have to do with the answer?
@ Lynx 33: That answer was posted before he received a Maractus, possibly?
There was an episode were the character of the day had three maractus. The only ones yet to appear I believe are genescect, who'll soon get a movie, and the x and y pokemon if I'm correct.
Cilan, as far as bulbapedia knows, has no maractus in the anime ( only in the game)
i have seen embor serpireor and some of the others in the anime
This is an old and outdated question
This answer is wrong
it's only wrong because it's old.
I would down vote you if I could!
Can´t you see the comments? It´s because it´s old
serperior purrlion simisage unfezant boldore gurdurr seismitoad throh sawk whimsicott lilligant krookodile crustle sigilyph tirtouga carracosta garboarder cinccino gothirita duosion reniculus vinilish vanilluxe karrablast amoonguss jellicent ferroseed ect all of em have been seen in the amine AND the movies dude AND some of the ledgends have been seen in THE anime like the weather trio
This question is four years old, of course there's going to be some Pokémon missing.
Braviery has. So have Genesect (Its in one of the FILMS) Stoutland has. (How did you not know stoutland. They made a huge scene of it DYING)
@AnonPokePlayer This answer was last updated in 2012, so many things are outdated.