If alternative phenotypes in polymorphic populations do not mate randomly, they can be used as model systems to study adaptive diversification and possibly the early stages of sympatric speciation. In this case, non random mating is expected to support genetic divergence among the different phenotypes. In the present study, we use population genetic analyses to test putatively neutral genetic divergence (of microsatellite loci) among three colour morphs of the lizard Podarcis melisellensis, which is associated with differences in male morphology, performance and behaviour. We found weak evidence of genetic divergence, indicating that gene flow is somewhat restricted among morphs and suggesting possible adaptive diversification.