PokéBase - Pokémon Q&A
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Like how you're on the GTS seeking Pokémon, it shows you everything you caught, even Pokémon that aren't in the Pokédex. Here's another example, When you're catching Pokémon, it puts a little Pokéball in the bottom right corner of the Pokémon's HP bar, even on Pokémon that aren't in the Pokédex, so is there an invisible National Pokédex? Where does the game record these Pokémon you catch that aren't in the Pokédex? Thanks in advanced.

Idk how to phrase this in a really potato way;
Not everything that is recorded or acknowledged in the game needs to be physically shown to you. The game is coded to recognise if you have caught a Pokemon or not quite simply, whether it exists on the physical 'Pokedex' or not.

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No there is not an invisible Pokedex per say, but it does know of all the 800+ Pokemon and keep track of all your caught Pokemon on sort of a list which is why it's able to keep track of which Pokemon to put that little pokeball next to.

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I guess I don't fully understand what you mean by invisible Pokedex, but I think that is what your asking
Thank you.