In insects, seminal fluid proteins that are produced by male accessory glands and transferred to females during mating have key functions in sperm competition and sperm physiology that lead to male reproductive success. In ants, male reproductive success also depends on the longevity of sperm stored in the queen’s spermatheca because their sexual offspring are usually produced only after a prolonged storage period. We identified genes that were up-regulated in the male accessory glands relative to the bodies of Crematogaster osakensis to characterize the reproductive molecules associated with male reproductive success in ants. We found novel genes that had no hits in a homology search and that were predominantly expressed in the accessory glands. These reproductive proteins may have evolved under rapid positive selection for reproductive success in the species. Furthermore, we discovered that three spermatheca-specific genes of C. osakensis queens were also enriched in the accessory glands relative to the bodies of males. These genes may be important for maintaining the sperm quality continuously from ejaculation by males to prolonged storage by queens. This research provides crucial information about the molecular mechanisms of sperm maintenance and sexual selection in ants, and also insight into the evolution of reproductive strategies in insects.