<p>The gotra system of exogamy is followed by the Brahmin caste group in India. This system restricts the marriage of individuals who belong to the same gotra. In genetic terms, each gotra forms an exogamous group within a population and thereby maintains a lineage. In Koṅkaṇī Sārasvata Brahmins, the gotras are patrilineal. To understand the genetic footprints of the gotras in this population, we reconstructed the maternal and paternal ancestry of 95 individuals using single nucleotide polymorphism (SNP) markers and Y-chromosomal short tandem repeats (Y-STR). The haplogroup distribution in the gotras showed a significant association with the paternal lineage (p &lt; 0.005) as compared with the maternal lineage. We observed a similar significant association of the gotras with the Y-STR haplotypes. Our findings provide scientific evidence for an actively existing gotra system followed by the caste groups of India. Comparative analysis of 334 Indian Brahmins and over 1300 Eurasian Y-STR profiles showed that all Brahmin groups share a common R1a ancestor with Western Iranian males likely predating the Indo-Iranian split in northern Afghanistan. Whilst North Indian Brahmins shared the lineage with Afghanistan groups, the Koṅkaṇī and southern Brahmins may represent an earlier divergence. The persistence of common gotras throughout India implies the gotra system originated before Brahmin dispersal from north to south. These findings provide genetic evidence for the role of gotra system in shaping Brahmin population structure.</p>