They wear dark blue. Why dark blue, you may ask, instead of black? Because if they wore black their silhouette would be able to be seen in the dark.
But it wasn't always dark blue. Other colors were worn, though less commonly like red, brown, dark green. etc.
Green and brown is used the forests to attack a target below from above a tree.
Red can't be seen in the dark as well. If a ninja was suddenly seen wearing all red that would strike fear in to there hearts due to the likeness of blood.
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