With an impressively wide distribution, Gehyra mutilata is present on almost all Indian and Pacific Ocean islands and in large regions of Southeast Asia and Indonesia. Mitochondrial sequence data (~500 bp) from individuals covering large parts of its (mainly insular) distribution reveals deep cryptic variation and strong geographic structure, with two well differentiated lineages. Molecular data also reveals that the wide Indian and Pacific insular distribution of Gehyra is very recent and, at least across the Indian Ocean islands, most probably the result of human-aided dispersal, as no variation within this lineage was found. Further research is needed to determine geographic patterns of variation across Southeast Asia, the level of genetic variation, and possible mechanisms of speciation. If recognized as distinct taxa, the binomen Gehyra insulensis should be resurrected, and applied to the ‘Pacific lineage’.