The Chinese water deer (Hydropotes inermis) belongs to a relatively early-divergence lineage of Cervidae and is thought to have retained some ancestral features of the group. This species is classified as Vulnerable on the IUCN Red List (accessed 2020), and populations in its native range have declined drastically in recent years.  However, a number of individuals were introduced to the UK about a century ago; these have flourished and now make up over 40% of global numbers.  To infer the population genetic structure and genetic diversity of Chinese water deer both in their native China and in populations introduced to the UK and France, mitochondrial DNA sequence variation was investigated (control region and cytochrome B) for near 100 individuals. The distribution of haplotypes among the regions shows distinct geographic structure, and only one cytochrome B haplotype was common to both China and European populations. Our results reveal lower levels of genetic diversity in the British populations, differentiation between native and introduced populations, and that the source population of British deer is likely to be extinct. Some recommendations are made for the conservation of different populations.