PokéBase - Pokémon Q&A
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To calculate rarity I use this criterea:

How low is its encounter rate, without it being a limited amount of encounters

So we disqualify legendaries and gift Pokemon

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https://pokemondb.net/pokebase/268258/what-are-all-of-the-pokemon-with-a-1-encounter-rate
There are no encounters below 1% that are infinite encounters, so these are the lowest.  It's in the last answer.

1 Answer

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If you look at the source Jhnfui got, here are the list of Pokémon in XY with a 1% encounter rate.

Abomasnow- Route 17

Flabebe White Flower- Routes 4 and 7

Lapras- Route 10 and Azure Bay while surfing

Pumpkaboo Super Size- Route 16 in the tall grass

Rotom Forms (not base form Rotom)- Lost Hotel and Shaking Trash Cans on Tuesday (if you look at the source, the answerer isn’t sure if this is a 1% encounter rate, it’s assumed)

Source

Hope this helps! :)

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