PokéBase - Pokémon Q&A
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For example, as far as I know, only zygarde has access to Aura Break. How many of these "indigenous" abilities exist, and which Pokémon have them?

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Best answer

Air Lock - Rayquasa
Aura Break - Zygarde
Bad Dreams - Darkrai
Color Change - Kecleon
Dark Aura - Yvetal
Delta Stream - Mega Rayquasa
Desolate Land - Primal Groudon
Fairy Aura - Xerneas
Flower Gift - Cherim
Forecast - Castform
Fur Coat - Furfrou
Imposter - Ditto
Multitype - Arceus
Parental Bond - Mega Kangaskhan
Primordial Sea - Primal Kyogre
Slow Start - Regigigas
Stall - Sableye
Toxic Boost - Zangoose
Victory Star - Vicitini
Wonder Guard - Shedinja

Source: http://pokemondb.net/ability

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Flaf, you missed the ones which are unique to a certain evolution line. Assuming ofc, those count
I only included Abilities with a single wielder, families excluded.
Forecast - Cherim?
I thought wonder guard was shedinja
1 vote

55 Pokemon

Upto ORAS there are 55 Pokemon with Signature Abilities.
See here for all the Signiture Moves

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The list is wrong. Many Pokemon share those abilities.
No it's technically correct. It counts Pokemon from every generation, not just Gen VI.