We report on a comparison of the genetic diversity between Ibiza and the population of the other Balearic islands and also between the archipelago with respect to circum-Mediterranean populations. For such a comparison, autosomal and Y-chromosome STRs, as well as mtDNA sequence data analyzed from the same individuals, were studied. Analysis of 14 autosomal STRs showed that Ibiza had significant differentiation with respect to other Balearic populations and also with respect to insular and continental populations from the Mediterranean area. Nevertheless, the results obtained from the analysis of eight Y-STRs showed a high level of genetic homogeneity for eight western Mediterranean populations. On the other hand, these populations did not show a compacted group when mtDNA diversity was analyzed, since they showed genetic differentiation among them. The analyses of haplotypes shared between populations indicated that mtDNA haplotypes have drifted to higher frequencies than the Y chromosome. This fact could be due to a shared recent history between Ibiza and other western Mediterranean populations, with numerous male displacements originated by wars and, especially, commercial relations. The results of mtDNA from the Ibiza population could be due to a maternal Carthaginian/Phoenician founder effect, together with genetic drift, in accordance with the historical and demographic data of the area.