Culex (Cx.) tritaeniorhynchus is a mosquito species with an extensive and expanding inter-continental geographic distribution, currently reported in over 50 countries, across Asia, Africa, the Middle East, Europe and now Australia. It is an important vector of medical and veterinary concern, capable of transmitting multiple arboviruses which cause significant morbidity and mortality in human and animal populations. In regions endemic for Japanese encephalitis virus (JEV) in Asia, Cx. tritaeniorhynchus is considered the major vector and this species has also been shown to contribute to the transmission of several other significant zoonotic arboviruses, including Rift Valley fever virus and West Nile virus. Significant variation in vectorial capacity can occur between different vector populations. Obtaining knowledge of a species from across its geographic range is crucial to understanding its significance for pathogen transmission across diverse environments and localities. Vectorial capacity can be influenced by factors including the mosquito genetic background, composition of the microbiota associated with the mosquito and the co-infection of human or animal pathogens. In addition to enhancing information on vector surveillance and potential risks for pathogen transmission, determining the genetic and microbial diversity of distinct populations of a vector species is also critical for the development and application of effective control strategies. In this study, multiple geographically dispersed populations of Cx. tritaeniorhynchus from countries within Europe, Africa, Eurasia and Asia were sampled. Molecular analysis demonstrated a high level of genetic and microbial diversity within and between populations, including genetic divergence in the mosquito CO1 gene, as well as diverse microbiomes identified by 16S rRNA gene amplicon sequencing. Evidence for the detection of the endosymbiotic bacteria Wolbachia in some populations was confirmed using Wolbachia-specific PCR detection and sequencing of Wolbachia MLST genes; in addition to PCR-based detection of insect-specific viruses. Laboratory vector competence showed Cx. tritaeniorhynchus from a Greek population are likely to be competent vectors of JEV. This study expands understanding of the diversity of Cx. tritaeniorhynchus across its inter-continental range, highlights the need for a greater focus on this invasive vector species and helps to inform potential future directions for development of vector control strategies.