Ayu (Plecoglossus altivelis) is a valuable economic fish in Aisa. The difference between males and females is obvious. Females have better growth traits than males, with faster growth and larger individuals. The market price of female fish is more than twice that of male fish. Therefore, the identification of the sex of ayu is extremely important to the economic value of breeding. To identify potential Sex-related genes in male and female ayu transcriptomes, the transcriptional profiles of sexual glands were extensively analyzed.