AbstractViñas, J., Pérez-Serra, A., Vidal, O., Alvarado Bremer, J. R., and Pla, C. 2010. Genetic differentiation between eastern and western Mediterranean swordfish revealed by phylogeographic analysis of the mitochondrial DNA control region. – ICES Journal of Marine Science, 67: 1222–1229. Despite there being evidence of several discrete breeding grounds, Mediterranean populations of swordfish have been considered a single panmictic unit with no genetic substructure. Sequence analysis of the mitochondrial DNA (mtDNA) control region of five Mediterranean locations (n = 251) reveals for the first time a clear genetic differentiation between eastern and western Mediterranean populations. This differentiation was detected only after conducting separate phylogeographic analyses on two previously described mtDNA clades. Although the frequencies of these clades are similar throughout the Mediterranean Sea, the levels of intra-clade genetic variation drop substantially towards the eastern end. This, together with clear differences in past demographic history and uneven migration rates between Mediterranean basins, suggests that the two populations experienced different effects during the Pleistocene. Subsequently, the mtDNA distinctiveness of eastern and western Mediterranean swordfish populations has been maintained probably by homing towards breeding areas.