The presence of Wolbachia in cardamom thrips (Sciothrips cardamomi), a major insect pest of cardamom (Eletteria cardamomum) was detected by amplification of the fast evolving outer membrane protein coding gene wsp of the bacterium. Studies on the identity of Wolbachia showed infection with only subgroup Con belonging to supergroup B, and both male and female thrips were infected with the same Wolbachia subgroup. The incidence of Wolbachia infection varied from 15.0 to 87.8% in thrips collected from seven cardamom growing districts of different States in India. The overall infection rate was 53.5% with 57.1% male and 50.6% female populations infected with the bacterium. DNA sequencing and phylogenetic analysis revealed that all the Wolbachia isolates from thrips clustered together indicating that all thrips were infected by the same Wolbachia strain. This is the first ever report of Wolbachia infection in cardamom thrips and the possibility of using the bacterium as a tool in biological control of this important insect pest is discussed.