Regional Dexes
In Pokémon 3D each available region (Johto, Kanto, and the Sevii Islands) has a local regional Pokédex documenting the Pokémon available within that region. This means that there are overlaps between each region as some Pokémon are available in all known regions, others in only 2, and many in only a single region. Catching a Pokémon in one region registers it for all regions (unless there are distinct regional forms involved).
Overview
Johto
This dex is received from Professor Oak at Mr. Pokémon's house on Route 31 with the Pokédex itself.
Kanto
This dex is received from Professor Oak in Olivine City before boarding the S.S. Aqua to Kanto for the first time.
Sevii Islands
This dex is received from Professor Oak's Aide in Vermilion City before boarding the Seagallop Ferry to the Sevii Islands for the first time.