Sequences from complete mitochondrial control regions (mtDNA CR) were usedto infer phylogenetic relationships in 25 Cervinae taxa. Cervus splits intoclades that are partially discordant with current speciesdelimitations. Nominate Cervus elaphus includes two divergent cladesthat must be referred to as species elaphus (European elaphoid deer)and canadensis (Eurasian and North American wapitoid deer). Cervusnippon splits into Japanese and continental plus Taiwan sika. PèreDavid's deer is nested within Cervus, suggesting that Elaphurus shouldbe merged with Cervus. European and Persian fallow deer are geneticallydivergent and distinct species. Sequence length varied due to a CR-Iinsertion, tandemly repeated twice in rusa and sambar deer, sika andwapiti, and repeated up to six times in a clade of Japanese sika. Variablecopy numbers of this repeat are also fixed in different sika subspecies,and could be used as a diagnostic marker for subspecies. Sequencevariability at the mtDNA CR is informative for defining species andsubspecies boundaries, and for locating the geographical origin ofcaptive-reared stocks. Natural and farmed populations of some specieshave been deeply affected by human management and the conservation ofdeer populations would be aided by the appropriate identification ofthe different evolutionary and taxonomic units.