| Summary: | <i>Gekko japonicus</i>, i.e., Schlegel’s Japanese Gecko, is an important species which is widely distributed in East Asia. However, the information about population genetics of this species from China remains unclear. To address this issue, we used sequences from a fragment of the mitochondrial protein-coding gene cytochrome c oxidase I to estimate genetic diversity, genetic structure, and historical demography of <i>G. japonicus</i> populations from China. Phylogenetic analysis indicated that <i>G. japonicus</i> had a close relationship with <i>Gekko wenxianensis</i>. A total of 14 haplotypes were obtained, of which haplotype 1 was the most common and widely distributed. The genetic diversity of <i>G. japonicus</i> was comparatively low across different geographic populations. The populations of <i>G. japonicus</i> were divided into four groups which exhibited low levels of genetic differentiation, and expressed an unclear pattern of population structuring. In addition, potential population expansion of <i>G. japonicus</i> has occurred as well. Overall, these results demonstrate that the populations of <i>G. japonicus</i> reveal low genetic diversity in China, which is attributed to the founder and bottleneck events among populations. Our results will provide meaningful information on the population genetics of <i>G. japonicus</i> and will provide some insights into the study of origin of populations.
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