The National Pokédex contained 386 Pokémon species after Generation III.
Generation III began with Pokémon Ruby and Sapphire, released for the Game Boy Advance in 2002. These games introduced 135 new species, starting with Treecko at National Pokédex number 252 and ending with Deoxys at number 386.
The total combines the 251 species from Generations I and II with Generation III’s 135 additions. It is therefore a National Pokédex total, not the number of Pokémon available in every individual game. Ruby and Sapphire initially restricted access to many earlier species, which sometimes causes players to confuse regional availability with the overall species count.
Pokémon Emerald, released in 2004, also belongs to Generation III and added story and gameplay changes without creating a new generation of species.