Hemidactylus flaviviridis was found at the Narita International Airport in a cargo that arrived from Shanghai, China. The specimen was identified using morphological and molecular techniques. The species is distributed from the Indian subcontinent to northeast Africa and has not been previously reported from Shanghai or from other parts of eastern China. Comparison of the mitochondrial NADH dehydrogenase subunit 2 gene sequence of this individual with available data revealed that the sequence to be identical with that of the homologous gene of H. flaviviridis from Dubai, United Arab Emirates, but differed by 2.9–4.0% uncorrected p distance from conspecific samples obtained from India and Pakistan, suggesting indirect transportation of the gecko individual from around Dubai to Japan, via Shanghai. This finding highlights future risks of colonization of exotic geckos to the warm temperate and subtropical regions of East Asia.