Pigmentation are special phenotypic traits in fish. Pigmentation variation of fish has been used as a very important research topics in genetics, evolutionary biology and developmental biology. Especially, the study of pigmentation in fish has been sharply accumulated by means of rapid development of molecular biotechnology. In this paper, I briefly summarized the chromatophore development and types, genetic basis of pigmentation variation in fish, and molecular mechanism of fish pigmentation. The aim was to provide an insight into molecular genetic basis of pigmentation in fish.