Abstract. 1. Tropical rainforest fragmentation may increase the risk of extinction of limited dispersers such as soil-feeding termites which play a fundamental role in soil structure and fertility. 2. We tested the hypothesis that population genetic structure of Labiotermes labralis, one of the most abundant soil-feeders in the Amazonian primary forest, may vary in response to local ecological conditions. 3. As a pre-requisite, two factors that may have important consequences on population genetic structure were examined: colony social organisation and infection by Wolbachia bacterium. This cytoplasmic endosymbiont is able to manipulate arthropod reproduction and thus, to alter patterns of mtDNA variation. 4. Three sites in French Guiana showing variable level of forest disturbance were studied. Three hundred and thirty-eight neuters and 14 primary reproductives from 17 colonies were genotyped using six microsatellites to analyse colony and population genetic structure. Moreover, one sequence of the COII mitochondrial gene was obtained for each nest. 5. We showed that all nests were monogamous. In a single site, all nests were infected by the same Wolbachia strain. This pattern of infection was not associated to a particular mitochondrial haplotype. 6. In the most disturbed site, a significant inbreeding coefficient associated with high relatedness between primary reproductives suggested that anthropogenic habitat fragmentation has induced genetic isolation of the population; a result reinforced by the mitochondrial data. Thus, habitat fragmentation might have serious consequences for the persistence of L. labralis populations in French Guiana.