Recent studies of the genetic structure of stream-dwelling organisms have suggested that fine-scale patterns are the consequence of patchy recruitment from a small number of matings and limited in-stream dispersal. Predictions of this hypothesis were tested by spatial and temporal analysis of the genetic structure of populations of a stream mayfly (Bungona sp: Baetidae) in subtropical streams in south-eastern Queensland. Significant departures from Hardy-Weinberg proportions occurred more often than would be predicted by chance alone and no consistent pattern was observed across sites, loci or sampling times. As in previous studies, the largest differentiation was observed at the smallest spatial scale (reaches within streams) on most sampling occasions. These data provide additional support for a patchy recruitment hypothesis. Despite the fine-scale population structure, there was evidence of widespread adult dispersal across the study region, especially between streams and subcatchments within the same block of continuous dense forest.