Abstract: Coral reefs, which have important ecological functions such as spawning and rearing, are the key habitats of marine fish. In this study, COI (Cytochrome c oxidase subunit I), part of mitochondrial DNA, was used as a marker to identify the fish eggs in Meiji Reef, and the species composition and the characteristics of seasonal variation were analyzed. The study shows that there were 37 species of fish eggs in Meiji Reef, belonging to 3 orders, 23 families and 31 genera. Most species (33 species) were successfully identified to species level while 4 species were just identified to genera level. Fish eggs mainly belonged to Perciformes (91.89% of species, 97.31 % of total number). The main ecological type of fish eggs was reef-dwelling group (72.97%). The density of fish eggs was 0.95 ind.·m^–3 in spring and 0.54 ind.·m^–3 in autumn. The dominant egg species was defined as having a dominance degree greater than 0.001. The dominant roe species in spring were Pterocaesio tile, Pentapodus caninus, Upeneus tragula and Cephalopholis miniata. And the dominant roe species in autumn are Thunnus albacares and Scolopsis taenioptera. The species replacement rate of fish roe in Meiji Reef between spring and autumn was as high as 94.59%. The indices of average taxonomic distinctness of spring and autumn were 53.63 and 50.77, respectively, and the indices of variation in taxonomic distinctness were 111.45 and 31.03, respectively. The results indicate that Meiji Reef is the spawning ground for a variety of commercial fishes and deep-sea fish and oceanic migratory fish (like T. albacares). The community structure of fish eggs in Meiji reef has obvious seasonal variation, reflecting that coral reef fish has high utilization of specific habitats.