We compared dispersal rates and patterns using both spatial genetic structure as well as direct measures of dispersal in Branchipodopsis wolfi, a freshwater anostracan inhabiting clusters of spatially fragmented and temporally unpredictable ephemeral rock pools in southeastern Botswana. For a total of 29 populations from three rock pool sites, the active population component was subjected to allozyme analysis for four loci and gene flow between populations was estimated. For a subset of the pools, we quantified the number of viable floating dormant eggs and larvae dispersing into overflow traps during flood events. Genetic and geographic distances were significantly correlated within each site. Gene flow estimates indicated from 0.6 to 227 migrants per generation. This relatively high effective dispersal rate corresponds with our direct observation of peak dispersal between pools during floods. Up to 784 viable dormant eggs and 301 larvae were trapped at one overflow during one single rainfall event. We determined that a distance of 50 m is already an effective barrier to gene flow for this species. There is ample effective genetic communication between different populations within each rock pool site, but this communication is limited by distance.