Wolbachia is a group of bacteria that is known to infect many arthropods and nematodes. It is one of the most common parasitic microbes and is possibly the most common reproductive parasite in the biosphere. The bacterium is best known for its ability to manipulate host reproductive biology where it can induce cytoplasmic incompatibility, parthenogenesis, feminization and male-killing. In the present study, onion thrips (Thrips tabaci Lindeman) were collected from 9 locations in India along with melon thrips (Thrips palmi Karny) and chilli thrips (Scirtothrips dorsalis). From the molecular level detection by using 16s rDNA, the Wolbachia infection has been detected in the onion thrips collected from 6 locations out of 9. Melon thrips and chilli thrips samples were also found to be infected by Wolbachia. The phylogenetic analysis revealed that all detected Wolbachia samples showed that all were distantly related to the previously known Wolbachia samples.