Among family Zoanthidae (Anthozoa: Hexacorallia: Zoantharia), Zoanthus and Isaurus are widespread benthos on coral reefs, but the reproductive biology of both genera is generally unknown. Accordingly, sexual reproduction of two Zoanthidae species in Japan, Zoanthus kuroshio in Okinawa, and Isaurus tuberculatus in Okinawa and Kochi, was investigated by annual sampling. Between 2012 and 2013, polyps of tagged colonies of Z. kuroshio and I. tuberculatus were sampled monthly, and gonads in mesenteries were examined under a stereomicroscope. In Z. kuroshio, sizes of oocytes were estimated and in situ spawning observations were conducted at night at Okinawa sites. Monthly sampling indicated that gametogenesis periods of both species in Okinawa were from May to August, and oogenesis set in earlier than spermatogenesis, and thus both species can be considered protogynous functional hermaphrodites. On the other hand, I. tuberculatus in Kochi had hermaphroditic polyps in July and August. Notably, fertile colonies of Z. kuroshio were not only hermaphrodites but also included exclusively male and female colonies. Overall, four sexual types were identified in Z. kuroshio: male, female, functional protogynous hermaphrodites, and unclassified sterile colonies. In situ gamete release of Z. kuroshio was observed in August 2012 and July to August 2013. First spawning of the year occurred 1 day after the new moon; colonies shed their bundles 3.5–4 h after sunset. We speculate that lunar phase and time after sunset influence spawning timing in Z. kuroshio. Basic knowledge on sexual reproduction of Zoanthidae is critically needed to better understand the basic biology of these benthic cnidarians.