Estuaries are important spawning areas for many freshwater and marine fishes. This is also the case for Baltic populations of European perch Perca fluviatilis, an important commercial species in the most of Europe. There is, however, inconsistency in the literature between the maximum salinity tolerance of the eggs in vivo, and the salinities at which some populations spawn in situ (7 vs. 9.6 ‰). In the present study, hatching success of perch was determined in vivo for a Danish, western Baltic, brackish water population at salinities of 4, 7, 10 and 12 ‰. Furthermore, in order to place the population genetically among other European perch populations, individual egg samples were sequenced for a 390 base pair fragment of the mtDNA Dloop region. Hatching occurred at all four salinities, with no statistical differences among treatments. Successful hatching at 12 ‰ is well above salinities of 7‰, which has previously been the highest reported from in vivo studies. This discrepancy is likely to be a result of methodological differences (e.g. different temperature) or perhaps interspecific variability in egg hatching abilities among perch populations. The perch from the present study consisted of a mixture of haplotypes similar to the haplotypes, known to dominate in the Central and Western Europe and the Baltic Sea regions. Our results highlight the potential for recruitment of perch in coastal waters in the western Baltic Sea and have implications for both coastal management and the aquaculture industry.