Mosquitoes have the potential to transmit a large variety of pathogens to humans and other vertebrate hosts. No effective technique has been found to properly control and reduce the density of mosquito populations in a sustainable manner. Endosymbionts, particularly Wolbachia, represent a promising al-ternative to control medically important mosquito species and reduce their disease transmission capacity. The presence of Wolbachia endosymbionts was screened in mosquito populations of Guade-loupe Island (French West Indies). Mosquitoes were collected across 39 sites that were representative of major biotopes in Guadeloupe and were categorized into natural, rural and urban landscapes. Natural and rural landscapes showed higher mosquito species diversity when compared to urban landscapes. The presence of Wolbachia was revealed by real-time PCR in six mosquito species belonging to five genera: Deinocerites, Culex, Mansonia, Ochlerotatus and Uranotaenia. Wolbachia was detected in mosquitoes collected at sites attributed to the three landscape categories. However prevalence of Wolbachia infection was heterogeneous among mosquito species and collection sites. Phylogeny based on Wolbachia surface protein (wsp) sequences showed that Wolbachia isolates from field collected mosquitoes were distributed across three major clades belonging to Wolbachia supergroups A and B. Some of the Wolbachia wsp sequences represent new haplotypes. The presence of Wolbachia in Neotropical mosquito species is expected to trigger new research on the control of mosquitoes and the pathogens they transmit. In mosquitoes, Wolbachia is able to re-duce the fitness and pathogen transmission, thus being a potential target for population reduction and replacement strategies.