In marine and freshwater invertebrate populations, microscale genetic differentiation or 'genetic patchiness' is thought to result from variation in the abundance and genetic composition of new recruits at a particular location. In the present study, the role of the adult emergence patterns in genetic patchiness was examined using mtDNA and two microsatellite loci to compare patterns of genetic differentiation in asynchronously (subtropical) and synchronously emerging (temperate) populations of the stone-cased caddisfly Tasimia palpata. A 550 base pair region of the mitochondrial cytochrome c oxidase subunit I gene (COI) was sequenced in at least 14 individuals from each population. Genetic structure was detected only at the reach scale in the subtropical populations and no genetic differentiation was detected in temperate populations. There were more deviations from Hardy-Weinberg equilibrium (HWE) in subtropical populations than in temperate populations where 44% and 12.5%, respectively, of tests for deviations from HWE were significant. Although distinct patterns of genetic structure and deviations from HWE were observed in the subtropical and temperate populations of T. palpata, no conclusive evidence was found to suggest that the differences are caused by differences in emergence patterns. We hypothesise that genetic patchiness must be caused by post-recruitment processes, most likely the preservation of oviposition 'hotspots' in subtropical streams.