PokéBase - Pokémon Q&A
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I think the question should be Do NPC's have shiny pokemon? because they can if GameFreak wants them to.
Flare come to chat PWEEZ PWEEZ PWEEZ? *Jumps up and down while shaking butt*

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They can only be shiny if they are pre-set in the game's coding meaning that there isnt a 1/1892 chance for a trainer to have a shiny Pokemon. They can only have a shiny Pokemon if it is pre-set. There are only three pre-set NPCs' Pokemon in the main games who have shiny Pokemon. They are only in FR/LG and there is a shiny meowth, espeon, and seaking in trainer tower.
There are also some NPCs who have shiny Pokemon in Pokemon Battle e
Source: http://bulbapedia.bulbagarden.net/wiki/Shiny

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