We used microsatellite markers to characterize the population structure of Coptotermes gestroi (Wasmann), an economically important termite species in the tropics. Eighty-five colonies were sampled from seven countries (Malaysia, Thailand, Singapore, Indonesia, the Philippines, Taiwan, and the United States [Hawaii]). Ten to 20 workers per colony were genotyped using eight variable microsatellite loci. STRUCTURE analysis partitioned the 13 spatially separated populations into four clusters. Individuals in the Peninsular Malaysia and Singapore population groups displayed admixture clusters. There was low genetic differentiation (F_ST = 0.073) among the Peninsular Malaysia populations, suggesting moderate gene flow among them. Comparatively, there was moderate genetic differentiation (F_ST = 0.192) and positive correlation between genetic distance and geographic distance among all of the 13 putative populations studied, which suggests limited gene flow among them. There was no significant isolation by distance within the three largest populations (Penang, Kuala Lumpur, and Singapore), presumably because humans aid the dispersal and fragmentation of colonies in these cities. However, significant isolation by distance was found in introduced populations (Taiwan). Population structure analysis demonstrated that C. gestroi populations in Taiwan were likely introduced from the Philippines.