Comparative phylogeography has revealed remarkable patterns of concordance in the maternal phylogenies of many species. The phylogeography and historical demography of the mitochondrial control region I for 607 Atlantic bluefin tuna (Thunnus thynnus) and 275 swordfish (Xiphias gladius) were analyzed to clarify the complex phylogenetic signals in the North Atlantic-Mediterranean region where they are sympatric. Atlantic bluefin tuna mtDNA is polyphyletic, and includes rare sequences sister to Pacific bluefin tuna (Thunnus orientalis) and introgressed albacore (Thunnus alalunga) sequences. There is no geographic partitioning between Atlantic and Mediterranean samples of Atlantic bluefin tuna (Phi(ST)=0.002). In contrast, Atlantic and Mediterranean swordfish are differentiated (Phi(ST)=0.091) due to the combined effects of vicariance, secondary contact, and dissimilar regional demographic histories. Mediterranean swordfish has substantially less variation, and a more recent history (tau=2.42) than that of Atlantic swordfish (tau=7.02). In spite of the discordant phylogenetic and phylogeographic signals, the demographic history of Atlantic swordfish and Atlantic bluefin tuna (tau=7.51) suggests concordance in the timeline of population expansion. Possible scenarios of cladogenesis, expansion, and contraction, influenced by glacial cycles during the Pleistocene, are formulated.