We used measures of genetic differentiation at seven allozyme loci to estimate the degree of movement of a stream invertebrate within and between catchments. Populations of Paratya australiensis, a common atyid shrimp, were sampled from three rainforest streams from each of two subcatchments in two adjacent drainage systems in southeast Queensland. Marked genetic differentiation was observed at all loci, suggesting extremely limited movement on a small spatial scale. This result is surprising given the widespread geographic distribution of P. australiensis in Australia, its great abundance in headwater streams in southeast Queensland, and the presence of a planktonic larval stage. Large differences in genetic structure occurred between streams, in some instances between those in the same subcatchment. Even larger genetic differences were seen between samples from streams in different subcatchments, with alternative alleles being fixed at different sites. The greatest differences were not, however, between the two drainage systems as predicted by the stream hierarchy model. This extreme spatial structuring was remarkably stable over a two-year period.