The present study made an attempt to observe genetic affinity of the Muslim population in South India with other neighbor populations. In this regard, DQB1 loci of HLA class II gene as a common genetic marker in phylogenetic assessment has been examined in 45 unrelated healthy individuals using sequence-based typing. The result of this study indicates a close genetic similarity among Indian sub-populations, in spite of segregation with other Muslim populations in North India. Although results of present study indicates genetic relationship of selected populations, all HLA loci or at least all loci of each classes to be assessed in order to attain highly probability of estimates.
