Molecular data from Cladopus and Hydrobryum, members of the aquatic angiosperm family Podostemaceae, were analyzed phylogenetically using the chloroplast matK gene and internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA (nrRNA) gene to infer the species relationships and the biogeographic history of the East Asian species. The phylogenies based on matK and ITS were incongruent for relationships in a northern clade of Cladopus, but the pattern of root morphologies (ribbon vs. linear) agreed with the matK phylogeny. The matK phylogeny revealed that all East Asian temperate species of each genus form a monophyletic group that is derived from tropical/subtropical species. A clock-constrained maximum-likelihood tree suggests that the divergence events of the temperate lineages from their tropical sisters occurred coevally in the two genera. Dispersal-vicariance analysis (DIVA) suggests that distribution at the middle latitudes was formed by a wide primary distribution covering tropical and temperate areas and a secondary dispersal event in Cladopus, and by a dispersal event in Hydrobryum. Two Kyushu-Fujian groups are found in Cladopus, one consisting of Japanese C. austro-osumiensis and Chinese C. fukiensis and another consisting of Japanese C. japonicus, C. austrosatsumensis, and C. doianus and Chinese C. chinensis, each of which shows little genetic differentiation between species from Kyushu, southern Japan, and Fujian, China, suggesting parallel biogeographic histories. Disjunct populations of Hydrobryum japonicum from Kyushu in southern Japan and from northern Thailand show little genetic differentiation, whereas a plant from Yunnan, China, diverged earlier than did the Japanese or Thai plants. The DIVA results suggest that the disjunctive distribution of Hydrobryum japonicum was formed by two dispersal events from Kyushu to Yunnan and to northern Thailand.