Small local populations may have low levels of genetic diversity, although widespread gene flow may counteract genetic drift and maintain high local diversity. At a larger spatial scale, a relationship between population size and genetic diversity could have important effects on the longitudinal genetic patterns in riverine corridors. We examined the genetic structure of 15 subpopulations of the caddisfly Hydropsyche orientalis in four rivers within the Natori River system in Japan using 78 polymorphic RAPD loci. Six subpopulations were fragmented by reservoirs and thus may be smaller, genetically isolated, or both. Pairwise F (ST) values were generally high throughout the study, and a higher mean value across the reservoirs (mean=0.219) relative to unfragmented streams 0.157) indicated reduced gene flow. Genetic diversity was not consequently reduced in these subpopulations; however, genetic diversity was positively correlated with larval density at all sites (percentage of polymorphic loci, %P = 46.3-59.1; expected heterozygosity H (exp) = 0.163-0.225). The longitudinal distribution of genetic diversity exhibited a unimodal pattern, with a peak in middle reaches. Correlation with larval density was a significant factor, although the presence of cryptic species as well as unimodally distributed environmental variables (e.g., habitat heterogeneity) provide alternative hypotheses. We suggest that studies examining longitudinal patterns of genetic diversity will provide a better understanding of the principal mechanisms that create and maintain biodiversity in rivers and streams.