Honmoroko Gnathopogon caerulescens is a critically endangered species and important for commercial fisheries; thus stock enhancement programs are being conducted to restore resources. We evaluated the genetic population structure of field collected samples including spawned eggs around spawning areas in Lake Biwa and the extent of genetic diversity in wild samples and hatchery stocks using sequences of mitochondrial cytochrome b gene. Pairwise I broken vertical bar st analysis and AMOVA clearly showed minimal population structure and haplotype network did not reveal any clear geographic pattern in Lake Biwa. It is probable that strays spawn in non-natal spawning areas, resulting in significant levels of gene flow among spawning areas. Genetic characteristics of hatchery stock F1, F2, and F3 were similar to those of wild samples in terms of haplotype diversity, nucleotide diversity and pairwise I broken vertical bar st values. These results indicate that the relatively high genetic diversity at its initiation was retained due to a lot of broodstock over two successive generations. Accordingly we propose that the current Honmoroko breeding method is appropriate for conserving the genetic diversity of Honmoroko and that the hatchery stock are genetically compatable for release and stock enhancement.