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Environmental conditions such as a pronounced salinity gradient and postglacial history make the Baltic Sea a suitable area for studying how selection and gene flow affect genetic differentiation in marine species. A cDNA library was used to identify new single nucleotide polymorphisms (SNPs) in Baltic populations of Mytilus spp. mussels. Sixty polymorphic SNPs were used to genotype 642 individual mussels from the inner Baltic, Danish Straits, northwest Denmark and a population of the northeast Pacific. We characterized 49 novel SNP markers that differentiate the populations of the North and Baltic Sea areas. Concordant narrow clines were observed at the entrance of the Baltic Sea for most of these markers. Considerable variance of hybrid index scores was observed in populations with intermediate allele frequencies within the hybrid zone, eg in Gedser and Hjelm. The presented results are in accordance …