Only some island populations of Podarcis sicula are hyperchromatic. The study of this phenomenon and its relationship with the lizards of the mainland and other islands, exhibiting a “normal” coloration, provides useful hints in our understanding of evolutionary mechanisms that have created the observed morphological variation. We performed a comparative morphological and genetic analysis of a hyperchromatic lizard population from Licosa Island, and compared the data with that obtained from normal-colored lizard populations both from Ustica and Cirella islands in the Tyrrhenian sea and from nearby mainland Italy. Morphological and microsatellite gene differentiation in the hyperchromatic Licosa population appears to have been much more rapid than the molecular evolution of the mtDNA. We discuss herein that the comparison of hyperchromatism and other types of morphological variation with molecular data in island populations of lizards may provide useful hints as to evolutionary mechanisms.