Phylogenetic relationships among 12 species of the genus Draco were inferred from 779 base pairs of mitochondrial 12S and 16S rRNA genes and allozymes for 20 presumptive loci. Results indicated the presence of at least four distinct lineages within the genus. The first lineage consists of D. volans and D. cornutus, whereas the second only of D. lineatus, which exhibits a great genetic divergence between two subspecies. The third is monotypic with D. dussumieri, the only species distributed in southern India. The fourth included all the remaining species. The third and fourth lineages are supposed to exclusively share a common ancestor. It is likely that the common ancestor of whole Draco originally diverged into three groups, the ancestors of the first, second, and third and fourth lineages, by vicariance. In the fourth lineage, D. blanfordii, D. haematopogon, D. melanopogon, D. obscurus and D. taeniopterus are likely to be exclusively close to each other. The resultant phylogenetic tree contradicts the dichotomous relationships previously hypothesized on the basis of morphological characters.