One of the primary unanswered questions regarding the dispersal of Romani populations concerns the geographical region and/or the Indian caste/tribe that gave rise to the proto-Romani group. To shed light on this matter, 161 Y-chromosomes from Roma, residing in two different provinces of Serbia, were analyzed. Our results indicate that the paternal gene pool of both groups is shaped by several strata, the most prominent of which, H1-M52, comprises almost half of each collection's patrilineages. The high frequency of M52 chromosomes in the two Roma populations examined may suggest that they descend from a single founder that has its origins in the Indian subcontinent. Moreover, when the Y-STR profiles of haplogroup H derived individuals in our Roma populations were compared to those typed in the South Indian emigrants from Malaysia and groups from Madras, Karnataka (Lingayat and Vokkaliga castes) and tribal Soligas, sharing of the two most common haplotypes was observed. These similarities suggest that South India may have been one of the contributors to the proto-Romanis. European genetic signatures (i.e., haplogroups E1b1b1a1b-V13, G2a-P15, I-M258, J2-M172 and R1-M173), on the other hand, were also detected in both groups, but at varying frequencies. The divergent European genetic signals in each collection are likely the result of differential gene flow and/or admixture with the European host populations but may also be attributed to dissimilar endogamous practices following the initial founder effect. Our data also support the notion that a number of haplogroups including G2a-P15, J2a3b-M67(xM92), I-M258 and E1b1b1-M35 were incorporated into the proto-Romani paternal lineages as migrants moved from northern India through Southwestern Asia, the Middle East and/or Anatolia into the Balkans.