In order to test the suitability of microsatellite markers to characterize brown trout populations, genetic variation at eight microsatellite loci was examined in nine samples of brown trout. Unbiased heterozygosity averaged 0.27 plus minus 0.17 in brown trout and the Atlantic samples showed the highest heterozygosity values (i.e., Bresle, 0.39 plus minus 0.11). A striking genetic differentiation was observed between populations, accounting for 52 per cent of the total gene diversity. The smallest genetic distances were obtained between samples of Atlantic origin, while the largest distances resulted between Atlantic samples and the sample from the Persian Gulf on one hand, and between Moroccan samples and Mediterranean samples on the other hand. These results suggest the existence of a major genetic subdivision in brown trout, in at least four genetic groupings: Atlantic, Mediterranean, Persian Gulf and North African. This subdivision is coherent with previous data calculated on protein-coding loci markers. Putative applications of microsatellites in brown trout evolutionary studies and management are discussed.