1. The recent arrival and explosive spread of the zebra mussel, Dreissena polymorpha (Pallas), in Ireland provided a rare opportunity to study the population genetics of an invasive species. 2. Eight polymorphic allozyme loci (ACO-1, ACO-2, EST-D, GPI, IDH-2, MDH, OPDH and PGM) were used to investigate genetic diversity and population structure in five Irish populations, and the results were compared with those from a previous microsatellite study on the same samples. 3. The mean number of alleles per locus (2.7 ± 0.1) was similar to the mean for the same loci in European populations, suggesting that Irish founder populations were large and ⁄ or multiple colonization events took place after foundation. A deficiency of heterozygotes was observed in all populations, but was uneven across loci. 4. Pairwise comparisons, using Fisher's exact tests and F ST values, revealed significant genetic differentiation among populations. The overall multilocus F ST estimate was 0.118 ± 0.045, which contrasted with an estimate of 0.015 ± 0.007 from five microsatellite loci on the same samples in a previous study. 5. Assuming that microsatellites can be used as a neutral baseline, the discordant results from allozymes and microsatellites suggest that selection may be acting on some allozyme loci, specifically ACO-1, ACO-2, IDH-2 and MDH, which contributed most to the significant differentiation between samples.