The Formosan subterranean termite, Coptotermes formosanus Shiraki (Isoptera: Rhinotermitidae), is primarily reported from subtropical and warm temperate regions, whereas Coptotermes gestroi (Wasmann) is reported from many areas of the tropics. Taiwan is one of a few areas where the distributions of the two species overlap. By analyzing partial mitochondrial sequences of COII, 12S rRNA, and 16S rRNA, we found that most Taiwanese C. formosanus populations were closely related to Japanese and some Chinese populations and that Taiwanese C. gestroi populations were most closely related to those from the Philippines and Hawaii rather than populations from Thailand, Malaysia, Singapore, and Indonesia. The intraspecific variation of C. formosanus was 0.7–0.8% for three genes among seven Taiwanese populations, whereas all Taiwanese C. gestroi populations had identical sequences. The results support that Taiwan may be a center of origin for C. formosanus, but a recent introduction site for C. gestroi.