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The blue coral (Heliopora coerulea, Pallas 1766) is a reef-building coral, which is recently been classified as a threatened species. Recent population genetic analyses have found two genetically distinct, cryptic lineages of this coral (types A and B). However, the ecological differences between them, as well as the drivers of this speciation, are still unclear. The aim of this study was to examine the possible differentiation in the reproductive timing of the two lineages, as a plausible cause of speciation. We subjected both formalin-and ethanol-preserved samples of the coral, collected from sympatric H. coerulea populations, for tissue and genetic analyses. Samples were collected every one or two months, from June 2014 to September 2017, around Sekisei Lagoon, southwest Okinawa, Japan. We also conducted field observations of the coral's reproductive behavior (larval brooding) in mid-June and July. As a result we could observe larval brooding behavior from mid-to late-July in type B; however no such behavior was observed in type A during the observation and sampling period. After examining a total of 468 histological samples, we found that the diameters of the oocytes and spermaries peaked from May to June in type A, whereas in type B they peaked from June to July, after which the spermaries disappeared or diminished. Our study demonstrates that the two H. coerulea lineages, under the same environmental conditions, exhibit different reproductive timings. This gap in reproductive timing, which possibly stemmed from endogenous differences, might have promoted their genetic differentiation and speciation into two distinct lineages.