The common tokay gecko (Gekko gecko gecko) is widely distributed across southern China, Vietnam and other countries in Southeast Asia. It includes two distinct morphological forms with largely allopatric distributions, which are referred to as the black-spotted tokay and the red-spotted tokay. Considering their different morphological features and distributions, a question has been proposed by taxonomists and still not resolved: do these two forms belong to one subspecies? Previous studies indicated a high genetic variability between them, but did not give a consistent conclusion regarding their taxonomic status. In this work, we employed two mitochondrial genes (cytochrome c oxidase subunit I and cytochrome b) and nine microsatellite DNA loci to explore the phylogenetic relationship and population genetic structure in the two forms from southern China and northern Vietnam. MtDNA results revealed four deeply divergent lineages. Red-spotted tokays were clustered into one lineage, and black-spotted tokays were clustered into three lineages. Microsatellite DNA results confirmed significant levels of genetic differentiation between the red-spotted tokay lineage and one black-spotted tokay lineage, consistent with the mtDNA pattern. In conclusion, considering both morphological and genetic information, we suggest that the red-spotted tokay lineage and one of the black-spotted tokay lineages have probably differentiated into two subspecies. However, more extensive sampling and genetic information are needed to further understand the taxonomic relationships of tokay gecko, particularly the three lineages within the black-spotted tokay.