Sequences of the cytochrome b gene were analysed for 47 samples of two species of Podarcis from the Balearic Islands (P. pityusensis from Pityuses and P. lilfordi, from Gymnesies archipelago). The average uncorrected distance between the two species studied was 9.7%. The sampled individuals from each species form reciprocally monophyletic units. Assuming an overall rate of change for cytochrome b of 2% per million years the nucleotide divergence of 9.7% ± 1.9% between P. lilfordi and P. pityusensis, could correspond to a divergence time of 4.95 ± 0.95 million years. The separation time between Gymnesies and Pityuses archipelagos according to geological hypotheses is around 5 million years, thus our results suggest the ancestors of the two present forms became isolated during this event. The most parsimonious networks suggest that currently accepted subspecies do not form monophyletic groups, and so should be reassessed. Despite our limited sampling the level of variability is much higher in P. lilfordi than P. pityusensis. Since they are sister taxa the relative age of each species is equal, therefore the differences might be due to historical population structure differences. However it seems that the forms on the islands are not genetically distinct units, implying that morphological differences are recent adaptations to their environments.