Most recently included in Pokémon Ruby and Pokémon Sapphire, the National Pokédex was created due to Nintendo changing the numbering scheme when they released the second generation of pokémon games.
The National Pokédex keeps with the classic numbering system as based in Kanto, a "province" of the Pokémon world that shares a similar name to an area around Tokyo, Japan. Although the terms National and Regional have no meaning in the real world as they are used in the "country" and "regions" in the video game world of Pokémon.
The numbering scheme begins at 001 and currently ends at 386. It differs from Regional Pokédex, where each region chooses its own method to number local species of pokémon and keep the more distant rare species towards the end.