Understanding Wolbachia mosquito interactions have been recognized as an important concept to develop novel vector control strategies. The prevalence of Wolbachia endobacteria in a natural population of the filariasis vector Culex quinquefasciatus was determined by the polymerase chain reaction method. Earlier workers had estimated the infection rates of Wolbachia with only one or very few individuals per species. In our study large number of specimens were assayed, and a total of 750 adult Culex quinquefasciatus mosquitoes were collected from three south Indian villages of Tirukoilur and Mugaiyur blocks, monthly for a period of five months (December 2006 to April 2007) and screened for the presence of Wolbachia. The percentage prevalence in adult males ranged from 88% to 96%; while in females from 84% to 100%. An overall prevalence of 91.2% was observed. There was no significant difference observed in the proportion of mosquitoes positive for Wolbachia between males and females, and also between different months of the survey; except during the month of February ‘07. The wsp gene sequence of the Wolbachia strain of Cx. quinquefasciatus detected was BLAST analysed and showed 99% sequence similarity with Wolbachia sp. of Culex pipiens isolated from different geographical regions. Phylogenetic analysis based on wsp gene fragments showed that the present Wolbachia isolate was closely related with Wolbachia from Culex pipens pipiens, Niphotettix virescens (Order: Hemiptera) and Cnaphalocrosis medinalis (Order: Lepidoptera).