The Asian subterranean termite (AST), Coptotermes gestroi (Wasmann) was described as a new record in Taiwan in 2003 by using soldier’s morphological characters. AST existence in Taiwan was confirmed by COII gene sequences in this paper. Both AST and Formosan subterranean termite (FST), C. formosanus Shiraki are invasive pests to Taiwan and Florida. FST distributed throughout the island of Taiwan and Florida peninsula, but AST was found only in the southern parts. By analyzing COII and 16S genes of Taiwanese Coptotermes spp, an undescribed species was discovered. The soldiers’ morphological characteristics of this C. sp. and C. gestroi are very similar, but the similarity between their COII genes is only 92%.