Background/Aims: The major histocompatibility complex (MHC) categorized into three (I, II and III) classes elicits the immunogenic response by presenting exogenous peptides to T cells. The MHC-II DM is composed of DMα and DMβ, two polypeptide chains, both are encoded by separate MHC genes involved in antigen processing and presentation. Despite the acknowledged role of MHC complex in humans, the literature is silent on the organization and expression of these genes in water buffalo Bubalus bubalis, an agriculturally important animal species. Methods: We deduced the full-length mRNA sequences of DMα and DMβ genes, localized them onto the chromosome 2, assessed their copy number per haploid genome and studied tissue and disease specific expression. Results: The Real Time PCR showed higher expression of both the genes and their seven interacting partners in spleen, gonads and spermatozoa. Significantly, upregulation of DMα and DMβ genes and their interacting partners were detected in diseased group of buffaloes as compared to that in healthy ones. Conclusion: The upregulation of Bubalus bubalis (BuLA)-DMα and DMβ genes and their interacting partners reflect their role in regulating immune responses towards the amelioration of diseases. Work on this line would enhance our understanding on the overall roles of MHC locus, allowing development of possible therapeutic treatment strategies.