The Asian subterranean termite, Coptotermes gestroi (Isoptera: Rhinotermitidae), is an important structural pest in southeast Asia, and it has invaded many regions of the world. Based on the combination of partial mitochondrial sequences of COII and 16S rRNA, phylogenetic analysis and genetic variation of C. gestroi populations from Hainan Island, Taiwan, and its native range were analyzed. The results showed that C. gestroi population from Hainan Island were closely related to those from Taiwan and the Philippines in southeast Asia. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation resided among geographical populations (82.8%), and Hainan, Taiwan, and the Philippines populations may form a single geographical group. The results suggested that C. gestroi has successfully on Hainan Island, and the Hainan population was likely introduced from the Philippines by humans.