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To fill something with color, as of the outlines of pictures in coloring books. A noun or pronoun can be used between "color" and "in." My daughter loves art, so just give her crayons and a coloring book, and she'll color in pictures all day long.
color something in
to paint or draw color on a pattern or outline. Here is a sketch. Please color it in. Color in the sketch, please.
To cover completely the bounded surface of something with a color: The child colored in an outline of a tree with green crayon. We traced the stencil and colored it in.