Ecological and phylogeographical investigations were made of disjunct populations of Deiratonotus kaoriae Miura, Kawane and Wada, 2007 in the Kumanoe (Miyazaki Prefecture) and Miyagawa (Mie Prefecture) Rivers, so as to compare life history patterns and elucidate genetic relationships between them. The relationship of carapace width with sex and occurrence of ovigerous females revealed a similar life history pattern throughout, new recruits occurring in spring and summer, reaching maturity the following autumn, and breeding in winter and spring. Large-sized individuals disappeared before the next breeding season, indicating longevity to be around 1.5 years. However, genetic analysis suggested an absence of present-day larval migration between the two populations. Two genetic groups present in the Miyagawa population were estimated to have diverged from the Kumanoe population in the Pleistocene.