In order to investigate the genetic diversity of the Bhutanese cattle, complete mitochondrial DNA displacement loop sequences from 30 Bhutanese cattle were determined and analyzed these in conjunction with previously published sequences. Sequence comparisons and phylogenetic analyses revealed the presence of B.taurus mitochondrial DNA haplotypes (13.3%), suggesting the genetic introgression of B.taurus genetic materials into Bhutanese population. The remaining B.indicus haplotypes indicated two clades of mitochondrial haplogroups, I1 and I2. The high frequency of I2 haplotype (46.2 %) was observed in Bhutanese cattle. Mean nucleotide divergence values were calculated within populations and Bhutanese population revealed higher value (0.75 %) than those of India (0.41 %) and China (0.19 %) . The results suggested the high genetic variability in Bhutanese cattle consisting of several haplogroups of mitochondrial DNA.