The existence of a genetic gradient across continents has often been highlighted. Comparisons among several genetic markers have suggested that most genes of current Europeans are descended from the Near East. During the Paleolithic period, populations were confined in refuges by the last glaciation. At the end of the Paleolithic period, European migrations began from these refuges. Our objective was to highlight these various flows, starting from well-defined isolated populations, originating mainly from western Mediterranean islands. We investigated polymorphisms in the hypervariable 1 (HVR1) zone of mitochondrial DNA (mtDNA) in many Mediterranean isolates: Andalusia, Balearic Islands, southern Corsica, Morocco, Sant' Antioco Island, San Pietro Island, Gallura, Nuoro and Trexenta (Sardinia) and Tuscany. We have compared our findings with those from other Mediterranean populations. Occupation of the Mediterranean area from the Middle East began in the Upper Paleolithic period around 40,000 years ago, with a population diversity determined by geographical and historical factors. Of the isolates studied, the population of the Balearic Islands show genetic characteristics correlated with various European flows initiated about 5,000 years ago. The island of San Pietro, in southwest Sardinia, still preserves the genetic traces of settlement by Ligurian migrants in 1736.