Seven microsatellite loci were recently described for the mayfly Baetis rhodani, but, at present, no data are available on the population structure of this species using these loci. We used four of these microsatellite loci for a preliminary analysis of the genetic differentiation of the mayfly B. rhodani in six populations from three Italian streams belonging to the same or different, but geographically distant, drainage basins. From these data, genetic polymorphism was observed between the sampled populations and clear differences were identified between pairs of populations; however, no specific population pattern was observed. The high F ST values suggest a limited dispersal of the species across the sampling sites. On the whole, the results obtained with microsatellite loci, characterized by marked heterozygosity deficiency, confirm the hypothesis of the patchy recruitment from a small number of matings and limited in-stream dispersal, as previously pointed out for some other baetid mayflies by genetic analyses using allozymes and mtDNA. This is the first contribution to a knowledge of the genetic structure of Italian Baetis rhodani populations.