Marine invertebrates release their gametes at an optimal time to produce the next generation. In reef-building scleractinian corals, synchronous spawning is essential for reproductive success. Molecular mechanisms of scleractinian gametogenesis have been studied; however, the mechanism by which coral gametes mature at specific times has yet to be discovered. The present study focused on two Acropora species with different spawning seasons. In Okinawa, Japan, Acropora digitifera spawns from May to June, whereas Acropora sp. 1 spawns in August. Comparative genomic analyses revealed that 60 genes are located in the diverged genomic regions between the two species, suggesting a possible association with timing of gametogenesis. Among candidate genes, we identified an Acropora sp. 1-specific amino acid change in gene WDR59, one of the components of a mTORC1 activator, GATOR2. Since regulation of gametogenesis by mTORC1 is widely conserved among eukaryotes, the difference in timing of gamete maturation observed in the two Acropora species may be caused by a substitution in WDR59 that slightly affects timing of mTORC1 activation via GATOR2. In addition, this substitution may lead to reproductive isolation between the two species, due to different spawning periods. Thus, we propose that A. digitifera and Acropora sp. 1 species pair is an effective model for studying coral speciation and understanding the molecular mechanisms that control coral spawning timing.