Two sequential year classes of Atlantic salmon parr, Salmo salar L., from 13 rivers throughout Ireland, genotyped at four widely used microsatellite loci, displayed comparable levels of intra-sample genetic variability to elsewhere in the species range. Temporal allele frequency differences were observed in only one riverine sample, whereas significant spatial differences were evident in all cases, with an overall F-ST value of 0.03. These spatial differences imply a high degree of natal homing. Two tributaries of a single major river system displayed variability comparable with that within the entire study, suggesting that large rivers may contain several separate tributary populations. Isolation-by-distance analysis suggests the presence of regional structure, which may have been obscured by inclusion of samples from some smaller rivers in Donegal Bay in the north west that are probably affected by incursions of cultured salmon from a nearby ranching operation. Although limited by the small number of loci screened, individual assignment analysis gave levels of self-assignment which would suggest that mixed stock analysis would be feasible as a management tool in Irish salmon fisheries, given the inclusion of larger numbers of microsatellite loci and more extensive coverage of salmon producing rivers.