PokéBase - Pokémon Q&A
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You start off the pokemon games with the regular pokedex, which only shows pokemon found in your region. For instance, in Pokemon black, the pokedex will only account for the Unova Pokemon. However, the national pokedex is a comprehensive pokedex that has every pokemon from every region. So using the same example, that pokedex that once had just the unova dex will now have every single pokemon to account for.

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thanks Dark Typhlosion