Control of mosquitoes is the most important aspect of public health, as mosquitoes transmit many human diseases, including the fatal infection, Japanese encephalitis. This paper addresses the isolation of new mosquitocidal bacteria from soil samples in the Union Territory of Pondicherry, India, where, no clinical cases of vector borne infections have been reported. Bacterial isolates from soil samples were screened for potential mosquitocidal strains and bioassays against mosquito vectors (Culex quinquefasciatus, Anopheles stephensi and Aedes aegypti) were carried out. Genomic DNA of potential mosquitocidal isolates was amplified and species identification was carried out using BLASTn program (NCBI). Phylogenetic analysis of 16S rRNA sequences of mosquitocidal bacteria revealed seven potential isolates. SDS-PAGE results have shown that there was considerable difference in the protein profiles. Numerical analysis revealed 4 distinct groups at similarity level 25%. The relationship between VBDs and prevalence of soil mosquitocidal bacteria in the study sites has elicited considerable interest in the diversity of mosquitocidal bacteria and their application for mosquito borne diseases control.