Sequences from complete mitochondrial control regions (mtDNA CR) were used to infer phylogenetic relationships in 25 Cervinae taxa. Cervus splits into clades that are partially discordant with current species delimitations. Nominate Cervus elaphus includes two divergent clades that must be referred to as species elaphus (European elaphoid deer) and canadensis (Eurasian and North American wapitoid deer). Cervus nippon splits into Japanese and continental plus Taiwan sika. Père David's deer is nested within Cervus, suggesting that Elaphurus should be merged with Cervus. European and Persian fallow deer are genetically divergent and distinct species. Sequence length varied due to a CR-I insertion, tandemly repeated twice in rusa and sambar deer, sika and wapiti, and repeated up to six times in a clade of Japanese sika. Variable copy numbers of this repeat are also fixed in different sika subspecies, and could be used as a diagnostic marker for subspecies. Sequence variability at the mtDNA CR is informative for defining species and subspecies boundaries, and for locating the geographical origin of captive-reared stocks. Natural and farmed populations of some species have been deeply affected by human management and the conservation of deer populations would be aided by the appropriate identification of the different evolutionary and taxonomic units.