Molecular population genetic diversity of two planktonic copepods of the North Atlantic, Calanus finmarchicus and Nannocalanus minor (Crustacea, Copepoda, Calanoida), was characterized using the sequence variation in a 350 bp region of the mitochondrial 16S rRNA gene. The subarctic species, C. finmarchicus, shows lower population genetic diversity (haplotype diversity, h = 0.368, SD = 0.043; nucleotide diversity, pi = 0.00370, SD = 0.0026) than the temperate/subtropical species, N. minor (h = 0.824, SD = 0.024; pi = 0.00502, SD = 0.0032). Effective population sizes (N(e), estimated from numbers of haplotypes) and effective female population sizes (Nf(e), estimated from nucleotide diversities) for the two species are 10(7) to 10(10) smaller than census female population sizes (Nf) estimated from observed densities and areal distributions. For both C. finmarchicus and N. minor, Nf approximately 10(15), N(e) approximately 10(8), and Nf(e) approximately 10(5). We hypothesize that the cause of both low levels of molecular diversity and small effective population sizes of the two species is the impact of glaciation during the past 20,000 years. C. finmarchicus may have experienced 75% range reduction and latitudinal displacement during the last glacial maximum at 18,000 years BP, giving rise to a genetic bottleneck; this may explain low diversity and an L-shaped distribution of pairwise haplotype differences. In contrast, N. minor may have experienced range reduction of only 30% and less change in latitudinal extent, with less impact of levels of molecular diversity and the shape of the pairwise difference distribution. Although marine zooplankton species are highly abundant, conservation biologists should note that their numbers may vary significantly on climatic to evolutionary time scales, generating low levels of molecular genetic diversity.