We sequenced mitochondrial DNA (mtDNA) from cytochrome b (cyt b) and the control region (CR) for all five extant species in the genus Tragopan. We incorporated information on comparative patterns and rates of molecular evolution into phylogenetic analyses, using both a single-gene and a combined data approach. Sequence variability was distributed heterogeneously among the three domains of CR and the three codon positions of cyt b, but the two genes evolved at comparable rates, on average, and produced concordant topologies independent of the method used for phylogenetic reconstructions. Phylogenetic trees suggest that Tragopan includes two main evolutionary lineages grouping caboti-temminckii (clade A), and blythii-satyra (clade B). A shorter CR sequence from one museum sample could not consistently resolve the position of T. melanocephalus. The mtDNA phylogeny is better supported than alternative topologies inferred from morphological and behavioral traits and is compatible with a mechanism of allopatric speciation of Tragopan in two different episodes about 4 and 2 million years ago. In those periods, the vicariant events that might have fostered allopatric speciation of Tragopan are represented by landscape changes that affected the Indohimalayan region after the sudden rising of the Himalayas less then 8 million years ago, and by climatic fluctuations during the Pleistocene less than 2 million years ago.