Wolbachia are a group of intracellular bacteria known to be prevalent among arthropods. Wolbachia infection cause declines of host populations, and also gives rise to host resistance to a wide range of pathogens. Over the past few decades, Wolbachia is used as a biological tool to control mosquito vectors. The study was aimed to identify Wolbachia strains in field collected St. albopicta from different breeding sites in Kerala. A total of 105 Samples were collected from 3 different areas with different breeding sites, areca nut planation in Kasaragod (North Kerala), rubber and pineapple plantation in Kottayam (Central Kerala) and tyres and containers in Thiruvananthapuram (South Kerala). The positive samples showing clear intensity were selected from general as well as strain specific samples for sequencing. The samples prior to sending for sequencing was extracted and purified using gel extraction kit and lyophilized. The sequences were aligned using ClustalW software. Then further phylogenetic analysis were made using MEGA 5 software. The positive samples were found to have 95% A(wAlbA) and B(wAlbB) super infection with 5% and 3% single infection of wAlbA and wAlbB strains respectively.