Relationships between species diversity calculated from Habitat Suitability Index (HSI) of aquatic animalms and genetic diversities of four species of aquatic insect (three caddisflies and one mayfly) were examined in the Natori River basin, middle of Miyagi prefecture Japan. The HSI has been evaluated for six riverine animals based on current velocity and water depth calculated from an existing distributed runoff model and geographical data (eg., landuse, slope, and urban ratio) by Kazama et al. (2007). As a result, three out of four genetic diversity indices of one caddisfly (Hydropsyche orientalis) showed significant positive correlation to the HSI based taxa richness. This result suggests a sharing influence of immigration on community and population levels is potentially high in the locations where many species can coinhabit. Accordingly, parallel effects of gene flow and habitat heterogeneity on species and genetic diversity through environmental filtering and local adaptation of genotypes of focal species would contribute to the enhancement of biodiversity.