The ecology of the freshwater life stages of the amphidromous shrimps Caridina leucosticta, C. typus and C. multidentata from southwestern Japan has been well studied. However, the ecology of their marine larval stages remains unclear. Therefore, to compare their genetic population structures and to predict their marine larval dispersal patterns, we collected 504 individuals of these 3 shrimps from throughout their distribution range in Japan and sequenced the mitochondrial DNA cytochrome c oxidase subunit I gene and control region. Comparative phylogeography showed that C. leucosticta had a genetically heterogeneous population structure, suggesting that the zoeal larvae remain near the river mouth, whereas C. typus and C. multidentata displayed homogeneous population structures, indicating high levels of larval dispersal. Consideration of these results alongside ecological data suggests a paradigm for amphidromous shrimps, whereby species with shorter larval stages require lower salinities for larval development and so cannot move with the ocean current, giving a narrower geographic distribution, whereas species with longer larval stages show the opposite pattern. We also detected species-specific demographic processes and local-scale population structures in relation to seascape features, which may have been shaped by the ecological features of each Caridina shrimp species.