Background: Wolbachia is an intracellular bacterial endosymbiont found in most insect lineages. In mosquitoes, the endosymbiont’s influence on host reproduction and arboviral transmission has spurred numerous studies aimed at using Wolbachia-infection as a vector control technique. However, there are several knowledge gaps in the literature and little is known about natural Wolbachia infection across species, transmission modes as well as the associations between various Wolbachia lineages and their hosts. This study aims to address them by exploring mosquito-Wolbachia associations and their evolutionary implications.Methods: We conducted tissue-specific PCR screening for Wolbachia infection in the leg, gut and reproductive tissues of wild mosquitoes from Singapore using the Wolbachia surface protein (wsp) molecular marker. Mosquito-Wolbachia associations were explored using three methods – a tanglegram, distance-based, and event-based method, and inferred instances of vertical transmission and host shifts. Results: Adult mosquitoes (271 specimens) representing 14 genera and 40 species were screened for Wolbachia. Overall, 21 species (51.2%) were found positive for Wolbachia, including Aedes (5 species) and Culex (5 species). Seven out of the 21 infected species were not previously reported: Aedes nr. fumidus, Aedes annandaelei, Uranotaenia obscura, Uranotaenia trilineata, Verrallina butleri, Verrallina sp., and Zeugnomyia gracilis. Wolbachia was predominantly detected in the reproductive tissues, an indication of vertical transmission. Despite this, Wolbachia infection rates vary widely within a mosquito host species. There is no clear signal of co-phylogeny between the mosquito hosts and the twelve putative Wolbachia strains observed in this study. Host shift events were also observed. Conclusions: Our results suggest that the mosquito-Wolbachia relationship is complex and that combinations of transmission modes and multiple evolutionary events likely explain the distribution of Wolbachia diversity observed across mosquito hosts. This has implications towards understanding Wolbachia’s diversity, ecology, and utility as a biocontrol method.