Two regions of the mtDNA of Atlantic herring (Clupea harengus), ND3/4 and ND5/6, were surveyed by RFLP analysis to assess the effects of marker variability on the power of statistical tests. Although haplotype diversity was similar, marked differences in the number of common haplotypes were observed between the two regions, with ND3/4 having a more even distribution of haplotype frequencies. ND3/4 also revealed higher differentiation among samples than ND5/6, similar to previously published microsatellite data of the same samples. The data suggested that the highly skewed haplotype distribution of many mtDNA markers may be one of the reasons for the less frequent detection of population differentiation compared to microsatellites. Pooling (`binning') of related haplotypes did not increase differentiation revealed by each mtDNA region individually, but greatly strengthened geographical patterns shown by both regions combined. The data provided evidence for genetic differentiation of Icelandic herring from other north-eastern Atlantic stocks, and indicated genetic differences between Baltic and Celtic Sea herring. However, mtDNA data failed to confirm previously reported differences between Barents Sea herring, Norwegian fjord populations and Norwegian spring spawners.