Hainan Eld's deer (Cervus eldi hainanus) experienced a dramatic decline in the late 1960s through early 1970s and by 1976 only 26 deer remained in Datian of Hainan Island, China. Since then, conservation efforts have successfully rescued this deer from extinction. We employed 10 microsatellite DNA loci to index genetic variation in the one source (Datian) and two introduced populations (Bangxi and Ganshiling) and suggest implications for the conservation of the species. A total of 40 alleles at 10 loci were examined from 198 deer blood samples. The source population harbored all 40 alleles, while the Bangxi and Ganshiling translocated populations contained 24 and 26 alleles, respectively. The genetic variability was low (He ≈ 0.33) for each of the three populations. No significant difference in genetic variability between the three populations was detected (P > 0.05); yet significant differentiation was found among the three populations. Our results suggest that founder effects and genetic drift have affected the two translocated populations. For conservation we recommend the three populations be managed as a meta-population. When establishing future reintroductions, the founder population should have a size larger than the original 26 founders in Datian population or be composed of a cohort of over 20 same-age individuals with 1:1 sex ratio. Genetic monitoring for both the source and translocated populations should be continuously conducted in order to assess the effectiveness of deer conservation in the future.