Genetic variation in samples of the endemicCrocidura siculaliving in Sicily and in two surrounding small islands, Marettimo and Ustica, was analysed by Random Amplified Polymorphic DNA fingerprinting (RAPD) and compared to morphometrics and external phenotypes. Molecular variation in the random sample of 99 DNA fragments of the Ustica shrews, showing.a melanic fur and a size‐shape variation in skull morphometrics, is of comparable size to that of the of northwestern and northeastern samples Sicily (Tufanio and Madonie). In the Marettimo shrews, bicoloured (grey and white) animals like those coming from Sicily and presenting a significant reduction in body‐size and skull morphometrics, molecular differentiation is higher than in those of the other locations, and characterizes this geographic population. Considering the paleogeographic records, it is hypothesized that the Marettimo shrews must have been isolated longer from the mother‐island; whereas for the Ustica shrews, a more recent arrival/isolations presumed. The RAPD results proved to be consistent with this reconstruction of theC. siculabiogeography. The Marettimo population, as opposed to that of Ustica, can thus be considered ‘one step further’ on the road of the speciation process. Melanism in the more recently isolated Ustica population does not parallel genetic differentiation and could emerge as an answer to the very strong selection and ecological adaptation in that volcanic insular environment. In any case, each population living in these two small islands off Sicily shows an independent evolutive divergence.