North Sea and Baltic Sea populations of the introduced polychaete Marenzelleria viridis (Verrill, 1873) reproduce at different times (spring and autumn, respectively). Enzyme separation by starch gel electrophoresis revealed major differences between specimens from the Baltic Sea and those from the North Sea (collected in 1992 and 1993) but a high degree of homogeneity among populations from the same sea. Three enzyme loci, glucose-6-phosphate isomerase (GPI-A, GPI-B) and malate dehydrogenase (MDH), were fixed to 100% by different alleles in the North and Baltic Sea populations, respectively. Different alleles are dominant for mitochondrial aspartate aminotransferase (mAAT) with allele frequencies of ca. 0.97 in all sampled populations from the North Sea and Baltic Sea, respectively, but heterozygotes were found in all populations. These genetic differences could be due to environmentally induced selection or genetically different origins of the populations, suggesting that populations of the genus Marenzelleria in the North and Baltic Seas may be two different species.