A study of the homogeneity between putative stocks of Phocoena phocoena in the North Sea and inner Danish waters was performed using isozyme electrophoresis. Two polymorphic systems, mannose phosphate isomerase (MPI) and phosphoglucomutase (PGM) were used in the analysis. A two-locus homogeneity test showed an effect of season and locality on the genotypic distribution. This led to a division of the total sample into season and into the two localities, the inner Danish waters (IDW) and the North Sea. The samples were then compared to the Hardy-Weinberg expectations where a deficit in heterozygotes was observed in the North Sea sample in both systems and at the Pgm locus in the total sample, indicating a mixing of sub-populations. A hierarchical contingency table analysis, also based on the genotypic distribution, showed a combined effect of season and locality and only an insignificant effect of sampling period, thus supporting the division into season and locality. The seasonal effect is further supported by earlier observations of a seasonal migration of harbour porpoises out of the Baltic in winter. A significant difference was observed between the two supposed sub-populations, IDW-summer and North Sea-summer samples, based on the genotypic distribution. This could also be a reflection of the sample sizes. On the basis of samples obtained from Canada, West Greenland and Holland a preliminary study of the population structure on a larger scale, comprising the North East and North West Atlantic, was performed. The results so far accord well with the hitherto accepted sub-populations of P. phocoena in the North Atlantic.