Coptotermes gestroi (Wasmann) (Blattodea: Rhinotermitidae) is a common economic termite pest widely distributed in Peninsular Malaysia. Nevertheless, research on C. gestroi is frequently employed in phylogeographic investigations using mitochondrial gene sequences that ceased to discuss further the population dynamics and colonization pattern. In this sense, the application of another highly variable molecular tool, such as microsatellite markers is suitable to effectively assess the population genetic structure of this invasive species. This study aims to identify and characterize seven microsatellite markers for the population structure analysis of C. gestroi. The seven microsatellite markers exhibited significant polymorphic characteristics with PIC values ranging from 0.7696 to 0.9609 (mean equal to 0.9009). A high homozygotes level has been found on Tm-Di08, Tm-Tr06, TmTe-07, TmTe08, and Tm-Pe9 markers, which leads to a higher estimation of null alleles and deviation from Hardy-Weinberg Equilibrium. All seven microsatellite markers were unlinked and distinct from one another and hence eligible for usage in this study. The population genetic study found significant inbreeding (FIT = 0.386, FIS = 0.281) within the C. gestroi individuals. The five C. gestroi populations were moderately genetically differentiated (FST = 0.141) but also relatively connected due to the moderate value of the relatedness coefficient (r = 0.204). Furthermore, the moderate degree of genetic variance (16 %) found among the populations in the AMOVA study supported the findings. A genetic structure study with PCoA and STRUCTURE revealed three genetic clusters. Pop1, Pop2, and Pop3 were separated into three different genetic clusters, while Pop4 and Pop5 have undistinguishable levels of groups for three genetic clusters respectively. In conclusion, the microsatellite markers were demonstrated as informative primers with polymorphic characteristics and can be utilized to study the genetic structure of C. gestroi population.