Culex mosquitoes are considered as one of the most important vectors of West Nile virus (WNV) and other arboviruses detected in at least 34 species of mosquitoes in the United States. This review paper summarizes previous studies on the genetic diversity of West Nile Virus vectors and focuses on population structure. In addition, it also attempt to review significant information about molecular markers used in investigating the geographical and temporal patterns of genetic diversity in Culex mosquitoes. Genetically independent markers are the best strategies for the correct identification of population demes, gene flow and species relationships when working with Culex mosquitoes. The apparently low or restricted gene flow of mosquito vectors may be due to the large geographic distance or isolation by distance and physical barriers to dispersal may explain the spatial pattern of current genetic diversity in some Culex species. On the other hand, other studies where gene flow is evident, the recognition of the existence of gene flow between populations provides useful information on their potential, and possibly of the infectious agent they transmit. The genetic structure observed in this study may lead to the best understanding of their genetic variations for the development of effective strategies for vector control.