Neocaridina denticulata is widely distributed in Asian freshwater waters. Because of its rich and varied body color, since 2003 this species has become an important ornamental shrimp. However, the pigmentation molecular genetics of N. denticulata sinensis is almost not reported. The genetic traits of red, yellow and transparent strains are very stable. In this study, many pigmentation genes were gotten by comparingthe skins transcriptomes of the three strains.