To clarify the reproductive ecology of the endangered cyprinid Honmoroko, Gnathopogon caerulescens, endemic to Lake Biwa, the occurrence of eggs in inlets, sex ratio and monthly changes in gonad somatic indices (GSI) were investigated in the Nishinoko lagoon, adjacent to Lake Biwa, from March to May, 2012. Eggs of Honmoroko were found on gravel and vegetation in two inlets, suggesting that not only the reed zone of Lake Biwa and its lagoons but also inlets of the lagoons are important spawning habitats of that species. The sex ratios of individuals collected in the two inlets were more malebiased (11.2–32.1 : 1) than that in the reed zone of the lagoon (1.5–2.7 : 1). The GSI of males gradually decreased as the breeding season progressed, those of females not showing any significant statistical changes, except for individuals collected around the reed zone and inlet in April. It was concluded that males remain in inlets and the reed zone during spawning, whereas females migrate to the inlets only for spawning, subsequently returning to the reed zone until the next spawning session.