Objective To analyze the DNA genetic diversity in SPF Jinding duck population using microsatellite markers. Methods The DNA genetic diversity in 71 SPF Jinding ducks were analyzed by microsatellite markers. Results A total of 152 alleles were detected at 17 microsatellite loci, and the numbers of alleles at each locus varied from 3 to 13. Thirteen microsatellite loci showed a high level of average PIC values (PIC > 0.5), the hererozygosity (H) was 0.5816±0.0142. Other loci showed a middle level of the average PIC values. Only 5 microsatellite loci were in Hardy-Weinberg equilibrium, although 12 microsatellite loci were not in (P < 0.01). Conclusions The results revealed that the genetic variabilities in the SPF Jinding duck population are rich, and this population meets to the genetic characteristics of the closed colony animals, so it can be used to establish the closed colony of SPF Jinding duck.