Here, we sequenced the complete mitochondrial genome of 29 Egyptian river buffaloes collected in two breeding stations of Egypt. The genome is 16,357-16,359 base pairs in length and contains the 37 genes found in a typical mammalian genome. The overall base composition is A: 33.1%, C: 26.6%, G: 13.9%, and T: 26.4%. Our analyses confirm that the mitochondrial genomes of swamp and river buffaloes are divergent (mean nucleotide distance ¼ 2.3%), and show that Indian river buffalo haplotypes cluster into three haplogroups, named RB1, RB2, and RB3 (mean distance ¼ 0.25-0.26%) and that the 24 Egyptian buffalo haplotypes fall into RB1 (with the Bangladeshi, Chinese and Italian buffalo haplotypes) and RB2.