Partial DNA sequences from three mitochondrial (cytochrome b, 12S rRNA and 16S rRNA) and two nuclear (β-fibrinogen intron 7 and C-mos) genes were used to estimate the phylogenetic relationships among all eight extant species of green lizards, Lacerta sensu stricto, and many currently recognized subspecies. All eight species form a monophyletic group. L. agilis, L. schreiberi and L. strigata are genetically well differentiated species. L. trilineata and L. pamphylica are not monophyletic units based on analyses of the β-fibrinogen intron 7. Lacerta media is closely related to some Lacerta trilineata. L. bilineata and L. viridis are closely related, and recognition of L. bilineata as a distinct species makes L. viridis paraphyletic also. For both L. bilineata and L. viridis, some subspecies appear to remain in their southern glacial refugia, while a single genetic entity shows successfully postglacial expansion. The topology derived from C-mos variation is concordant with that derived from mtDNA, with substitutions occurring at a similar rate to that of transversions in the rRNA genes. Although C-mos is typically used at deeper taxonomic levels it is also phylogenetically informative within green lizards. β-fibrinogen intron 7, typically used for assessing phylogenetic relationships among bird species, is a useful phylogenetic marker for reptiles also, showing considerable variation between species. There is not complete concordance between estimates of relationships derived from the mtDNA and nuclear markers, probably because rapid diversification led to incomplete lineage sorting in the green lizards. Introgression could also be occuring between some species.