The study on genetics of naturally colored cotton suggests that the fiber pigment are controlled by genes. The appearances of brown and green cotton of the fiber are dominated respectively by incompletely dominant single genes and incompletely dominant major genes. Production and accumulation of the fiber pigment are related to special expression of enzymatic genes for pigment synthesis in fiber cells. On the stage of fiber lengthening, naturally colored cotton, like white cotton, appears purely white. But when entering fiber cell wall thickening stage, a little pigment appears by degrees. When the fiber is matured completely(on boll dehiscence), the color turns into the darkest level. After wetting process treatment, hue of the fiber pigment all change in some regular patterns. As for brown cotton, the hue will change anti clockwise way with hue circle of brown and green cotton respectively. In general, the treated cotton color and luster will become dark and vivid, and this trend will provide a possibility for enhancing the fiber quality by suitable environmental friendly finishing. The analysis shows that the color and luster of the cotton may be controlled by a series of pigments which show a little different chemical performance.