These results indicated that sex-related genes, such as IAG, SXL, TRA-2, SRY, FTZ-F1, FOXL2, and cytochrome p450, might play important roles in maintaining the male physiology and morphology of Eriocheir sinensis. Ubiquitin, serpin, cathepsin A, and cathepsin D genes may have a direct influence on spermatogenesis.