['Species with habitat specificity show restricted distribution, and the limited dispersal provides opportunity for long-term isolation. Aquatic Podostemaceae grow on rocks in river rapids, which are extreme habitats for angiosperms. To infer the diversification process of the podostemad species in such specific habitats, we investigated environmental factors shaping their distribution and the relationship between their distribution and genetic structure.', 'We used Hydrobryum japonicum and Cladopus doianus, which have contrasting distributions (i.e., narrower and wider, respectively) in southern Kyushu, Japan. Environmental factors contributing to their distribution were estimated by ecological niche modeling. Using polymorphisms in chloroplast DNA, we performed population genetic analyses of 13 H. japonicum populations occurring in nearby river basins and eight C. doianus populations in distant rivers.', 'Estimation of distribution probability showed great contributions of geology and temperature to the distribution of these populations, suggesting that the species grow on volcanic rocks in relatively warm areas. Genetic analyses revealed higher interpopulational genetic diversity than intrapopulational diversity and strong differentiation between rivers in both species. No correlation between genetic and geographic distances was detected among the C. doianus populations, in contrast to the significant correlation observed in the H. japonicum populations.'] Does habitat specificity enhance genetic differentiation in two species of aquatic Podostemaceae in Japan?