The population structure of harbour porpoises from British and adjacent waters was studied by examining variability in a 200 bp (base pair) section of the control region of mitochondrial DNA (mtDNA) extracted from 327 animals. This region contained 20 variable sites giving rise to 24 different haplotypes. Mean nucleotide diversity between all pairs of haplotypes was 0.81 per cent (range 0–4 per cent). The most common haplotype occurred in 63 per cent of the samples and was recorded in all geographical areas; several other haplotypes were present in two or more of the sampling locations. This suggests considerable historical interconnections among populations, probably through gene flow. However, there were significant differences (p less than 0.05) as determined by AMOVA (Analysis of Molecular Variance, Excoffier et al. 1992), between porpoises from the northern and southern North Sea , and between the northern North Sea and the Celtic/Irish Sea. The differences were predominantly due to variation among females. This sex-related difference in population genetic structure suggests that males disperse more than females. This has important consequences for evaluating the consequences of incidental catches of porpoises by fisheries in these seas since there may be a greater impact on local populations than is implied by simple calculations of mortality.