This Article or Image Relates to the Non-Canon Game, Pikmin:Civil War.
Shadow pikmin are a type of pikmin found in Pikmin: civil war which are not able to be controlled. They are black with glowing red eyes and seem to be made a gas like substance rather than a physical being.
in the afore mentioned game, shadow pikmin (led by the Shadow queen) have turned pikmin against each other and attempting to kill all other colours. They are able to possess rogue pikmin (and do just this to the entire bulbmin race) as well as travel at lightning speed to ravage pikmin with its claws.
how to kill
The only way to defeat them is to use the elemental power ups. no physical attack will work.
Pikmin: Shadow Planet
In Pikmin: Shadow Planet, Shadow pikmin are completely black, even their leaf/bud/flower. Only their eyes are a different colour, grey. They will attack your pikmin when either you are attacked by them or your pikmin are turned into them. They, along with some other evil pikmin types, are commanded by Shadow Olimar.