The blue mussel, Mytilus edulis, and the Mediterranean mussel, Mytilus galloprovincialis, occur widely over much of northern Europe, and wherever they are sympatric they hybridize. The hybrid zone is large, ranging from western France to the north of Scotland, and is spatially complex, containing a mixture of pure, hybrid and introgressed individuals. Results from an Irish study in 1981, using partially diagnostic allozyme markers, indicated that mussels on the Irish Sea coast were solely M. edulis, but on Atlantic wave-exposed shores, and to a much lesser extent on wave-protected shores, mussels comprised an interbreeding mixture of M. edulis and M. galloprovincialis. In this study mussels were analysed from 20 locations on Irish coasts, using the Me15/16 nuclear DNA marker. The results showed a high frequency of M. galloprovincialis (0.378 ± 0.198) and hybrid (0.429 ± 0.175) genotypes, and correspondingly low frequencies of the M. edulis genotype (0.194 ± 0.107) at both exposed and sheltered locations on Atlantic coasts, indicating no apparent advantage for the M. edulis genotype at wave-protected sites. Mytilus galloprovincialis was virtually absent from the Irish Sea. Mussels in this area may be a self-recruiting population of M. edulis due to thermal front development at the northern and southern entrances to the Irish Sea in late spring, thereby preventing an influx of spring-spawned Mytilus larvae. The apparent change in the genetic composition of mussels on Atlantic coasts since the early 1980s could be related to climate change, or to aquaculture practice in Ireland whereby mussels from exposed shores are used to seed ropes in wave-protected bays and estuaries.