Abstract: In order to discuss the current status of breeding conservation in Wenchang chicken breeding farms and the better conservation of Wenchang chickens, a high-quality national livestock genetic resource, the experiment was conducted with 235 blood samples as research objects collected from healthy Wenchang chickens in three Wenchang chicken breeding farms in Hainan Province（corresponding breeding flocks were TN, LQ and CW）; the TN and LQ conservancies were 77 each, and the CW conservancy was 81. DNA from blood samples was extracted for genome resequencing, and single nucleotide polymorphism（SNP） was detected in the whole genome level by using GATK（V 4.1.6.0） software; expected heterozygosity（H_E）, observed heterozygosity（H_O）, nucleotide polymorphism（pi）, degree of linkage disequilibrium（LD）, population differentiation index(F_ST), genetic distance（D） and inter-population genetic structure were calculated or evaluated for each conserved farm population by using various analysis software. The results showed that a total of 11 541 878 SNPs loci were obtained after quality control and filtering. The TN conservancy had the highest H_E of 0.307 768; the LQ conservancy had the highest H_O of 0.298 206; the CW conservancy had a lower pi than the LQ and TN conservancies; the TN conservancy had the smallest decay distance and its population genetic diversity might be higher than those of the CW and LQ conservancies. The highest degree of genetic differentiation between the CW and LQ conservancies F_ST value was 0.015 415, while the lowest degree of genetic differentiation between the LQ and TN conservancies F_ST value was 0.007 829. The LQ and CW conservancies were genetically close within the population, while the TN conservancy was relatively distant within the population. All Wenchang chicken individuals were clustered into three categories; the overall genetic diversity of the Wenchang chicken conservancy population was relatively high, but there was a certain degree of genetic differentiation among the three conservancy populations, and each conservancy population had shown its own uniqueness. The results indicated that the lack of gene exchange among the breeding farms of Wenchang chickens might lead to a certain degree of inbreeding and deepening of differentiation. In the future, gene flow among breeding farms should be strengthened, while a reasonable matching system should be developed to avoid the reduction of genetic diversity within the population as much as possible and to better protect Wenchang chickens as an important resource.