The sequence polymorphisms at the mtDNA hypervariable regions I and II (HVR-I and HVR-II) were analyzed in 87 individuals belonging to three religious groups, Hindu, Muslim and Christians of Karnataka (South India). A total of 122 polymorphic sites were observed in the sequenced regions, with HVR-I exhibiting higher variation than HVR-II. The populations exhibited high sequence and nucleotide diversity, alike other studied caste groups of Karnataka.