Abstract: We studied the genetic differentiation of Goniurosaurus indet. from northwestern Guangdong Province, China, and its phylogenetic relationships with other Chinese species, using partial sequences of the mitochondrial 12S rRNA and 16S rRNA genes of 10 species in total and Gekko gecko as the outgroup. A total sequence of 862 nucleotides of 12S rRNA (385 bp) and 16S rRNA (477 bp) genes were analyzed; 388 variable sites and 123 parsimoniously informative sites were detected in combination of the two genes. Analyses of Bayesian inference (BI), maximum likelihood (ML), maximum parsimony (MP), and neighbor-joining (NJ) all showed similar results: a close phylogenetic relationship between Goniurosaurus indet. and G. yingdeensis (genetic distance = 0.044-0.046), comparable to that between accepted known species G. araneus and G. luii (genetic distance = 0.051). Combined with morphological differences, our results support the notion that there is significant genetic differentiation between Goniurosaurus indet. and G. yingdeensis even though the two forms are separated only by a river; thus, Goniurosaurus indet. may be a new species. The phylogenetic analyses also indicated the uniqueness of G. hainanensis with the greatest genetic distance from others, suggesting that the character state of four body bands including nuchal loop is plesiomorphic as compared to that of five body bands. Our study lends support to the known phylogeny of Eublepharidae and provides complementary data for the conservation of Goniurosaurus. We hypothesized for the first time that rivers act as isolatiing barrier for population differentiation and speciation among continental Goniurosaurus species.