Genetic structure among five populations of Elliot's Pheasant sampled from five different provinces – Anhui (AH), Zhejiang (ZJ), Fujian (FJ), Hunan (HN) and Guizhou (GZ) – was assayed using mitochondrial control region sequences from 33 individuals. Using AMOVA, we found a high level of haplotype variation within populations, and a degree of genetic structure among groups (GZ population relative to all others pooled). However, this difference was not statistically significant and little geographical structure was indicated among the remaining populations. Furthermore, using a rooted maximum parsimony tree, we found the sequences of the GZ population were largely grouped in their own branch, while sequences of the other four populations were interspersed among branches. We identified a lower level of gene flow between the GZ population and all others, a finding supported by significant FST values. Conversely, we identified a larger amount of gene flow between the remaining four populations, particularly among the three easternmost populations (AH, ZJ and FJ). Given our results, further study should be focused on the GZ population and on management units for the purpose of maintaining the genetic structure of the species in the west of China.