Origin and ancestry of the Badagas of Nilgiris, an indigenous community of Nilgiris, Tamil Nadu in India, is a controversial topic. During our massive screening for haemoglobinopathies among Badagas, we identified a rare south Indian haemoglobin variant, the haemoglobin D (Hb D) Punjab (HBB: c.364G>C; rs33946267). The observed Hb D cases were double heterozygous with sickle cell trait (HbSD-Punjab) and manifested symptoms. The beta-globin distal promoter motif (-530 cap site BP1U) sequencing revealed a characteristicheterozygous combination of Arab-Indian sickle haplotype ((AT)₉ (T)₅) with universally common beta gene haplotype ((AT)₇ (T)₇). The report is a pioneer one informing the presence of Hb–D Punjab from an indigenous or aboriginal group of southern India. By the above information, we support the theory of unicentric tribal origin and distribution during Harappan civilization.