Human leucocyte antigen (HLA) loci widely known for their role in generation of immune responses by encoding cell‐surface heterodimers are often considered to be effective for the purpose of reconstructing human phylogenies due to high degree of polymorphism and less recombination. In the present study, we have made an attempt to study HLA class II loci (DRB1, DQA1 and DQB1) in inferring phylogenetic relationship based on both phylogenetic and haplotype approach. In the phylogenetic approach, the compiled database of 19 populations got segregated and finely resolved in three basal clusters with very high bootstrap values corresponding to four geo‐ethnic groups of Africans, Orientals, Americans and Caucasians. Maximum‐ likelihood phylogram has placed North Indian Hindus alongside other Caucasian populations. Haplotype analysis revealed high range of haplotype diversity with nearly 144 observed haplotypes. The haplotype distribution suggested that numbers of Caucasian‐specific haplotypes are frequently found among north Indian Hindus. Our results indicate that if the property of less recombination is explored to assign extended haplotypes, followed by strong interpretation based on more logistic statistical model, then there is a high possibility that HLA class II loci can infer exact and accurate phylogenetic assessments as revealed by mtDNA and Y‐chromosome markers.