Thirteen specimens of Tarentola from the Cape Verde islands were sequenced for 695 base pairs of 12S rRNA and cytochrome b mitochondrial genes, and analysed with published sequences. Our results support many of the relationships previously proposed. We report the presence of Tarentola gigas Bocage, 1875 on São Nicolau and Tarentola caboverdiana nicolauensis Schleich, 1984 on São Vicente. This increases the number of genetically distinct forms on these islands; hence community structure appears to be more complex than previously understood. We also sequenced seven individuals for 375 base pairs of the nuclear gene, C-mos. Two sites were variable, much less than expected given the high levels of differentiation based on mitochondrial DNA sequences.