This study investigated the biogeography and genetic variation in the antitropically distributed Micromesistius genus. A 579 bp fragment of the mitochondrial coI gene was analysed in 279 individuals of Micromesistius poutassou and 163 of Micromesistius australis. The time since divergence was estimated to be c. 2 million years before present (Mb.p.) with an externally derived clock rate by Bayesian methods. Congruent estimates were obtained with an additional data set of cytochrome b sequences derived from GenBank utilizing a different clock rate. The divergence time of 2 Mb.p. was in disagreement with fossil findings in New Zealand and previous hypotheses which suggested the divergence to be much older. It, therefore, appears likely that Micromesistius has penetrated into the southern hemisphere at least two times. Paleoceanographic records indicate that conditions that would increase the likelihood for transequatorial dispersals were evident c. 2–1·6 Mb.p.. Haplotype frequency differences, along with pairwise FST values, indicated that Mediterranean M. poutassou is a genetically isolated population.