Guizhou golden monkey (Rhinopithecus brelichi) was a unique, endangered and endemic primate species in Guizhou Province. It was an isolated population caused by habitat loss and fragmentation due to the human disturbance in the recently 30 years in China, only distributed in Fanjingshan National Natural Reserve, Guizhou Province. To know the background with demonic population structure, we sequenced 867 bp of the mitochondrial DNA D-loop from 312 fresh fecal samples, results showed there 11 haplotypes among these samples, h was 0.517, π was 0.00413. It indicated that this species had the lowest genetic diversity among four golden monkeys in China and need strengthen the conversation concern for this species immediately.