Forty populations of Potamogeton pectinatus L. were sampled from around the Baltic Sea basin. Analysis of 62 ISSR ‘loci’ showed that the number of clones per population is very variable but shows a tendency to decrease with latitude. Analysis of molecular variance revealed that, overall, just over half the variability is stored within populations and just under half between them (φST 0.496). In pairwise comparisons, most populations are significantly differentiated. Genetic distance between populations, as measured by φST, increases with geographical distance. Levels of population differentiation, however, are lower on the southeastern Swedish coast than elsewhere, a reduction correlated with the importance of this area as a staging post for the massive migrations of waterfowl from arctic Russia and western Siberia. Cumulative plots of φST against geographical distance along this coast suggest that, although it does not prevent significant population differentiation, bird traffic reduces it over distances of 150–200 km.