A reservoir blocks the gene flow of stream macroinvertebrates along a channel, which takes place via larval drift and adult flight. We developed a model for stream macroinvertebrate populations to simulate genetic differentiation between fragments above and below a reservoir. The model includes parameters of population size, dispersal rate, mutation rate, and magnitude of habitat fragmentation caused by reservoir. According to the model, genetic distance (Nei's D_xy) between the fragments increased following dam construction, and finally reached maximum differentiation within 10-50 generations. We simulated genetic differentiation of caddisfly Stenopsyche marmorata (Trichoptera, Stenopsychidae) populations based on a data set of D_xy at 6 dam sites observed with Random Amplified Polymorphic DNA markers, and evaluated the proportion of individuals unable to migrate across the reservoirs due to the dam constriction. The result indicated migration was largely reduced (i.e., 20-60 % individual migrating) in 2 dams and was completely halted where D_xy was highest. Our study suggests the strong potential for individual-based population genetic model to enhance our understanding of genetic differentiation caused by anthropogenic habitat fragmentation such as dam construction.