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The Balearic archipelago (Spain) is composed of three major islands, Majorca, Minorca, and Ibiza. Majorca is the largest and most populous island. Minorca is the second largest in area and third in population, and Ibiza is the smallest of the three and has the second largest population. Ibiza also shows differences from the other two islands in its landscape, vegetation, and especially origins of the founding settlements. The three islands also have been settled by people of different cultures. We have carried out a genetic analysis at the level of mtDNA RFLPs in these populations and found that the three populations are genetically structured, with differences in the RFLP haplotype frequencies reflecting the different population substrata of the three islands. In this structure Ibiza is genetically more different from Majorca and Minorca. In addition, we found a new haplotype in Minorca, named haplotype 150, which seems to originate from haplotype 56.