Simple SummaryWenchang chickens are the only chicken breed listed in the ‘animal genetic resources in China (poultry)’ in Hainan Province and are famous for their excellent meat quality. Protection of this genetic resource may ensure poultry husbandry’s sustainable and successful development. For more effective conservation, development, and utilization of this genetic resource, we investigated the diversity, degree of inbreeding, and runs of homozygosity (ROH) patterns for Wenchang chickens using whole-genome sequencing data. Our analysis showed that the genetic diversity of Wenchang chickens was relatively high. Selection signal analysis of Wenchang chickens based on ROH found some candidate genes that were putatively associated with meat quality traits and stress resistance traits, such as disease resistance and heat tolerance.AbstractWenchang chickens, a native breed in the Hainan province of China, are famous for their meat quality and adaptability to tropical conditions. For effective management and conservation, in the present study, we systematically investigated the characteristics of genetic variations and runs of homozygosity (ROH) along the genome using re-sequenced whole-genome sequencing data from 235 Wenchang chickens. A total of 16,511,769 single nucleotide polymorphisms (SNPs) and 53,506 ROH segments were identified in all individuals, and the ROH of Wenchang chicken were mainly composed of short segments (0–1 megabases (Mb)). On average, 5.664% of the genome was located in ROH segments across the Wenchang chicken samples. According to several parameters, the genetic diversity of the Wenchang chicken was relatively high. The average inbreeding coefficient of Wenchang chickens based onFHOM,FGRM, andFROHwas 0.060 ± 0.014, 0.561 ± 0.020, and 0.0566 ± 0.01, respectively. A total of 19 ROH islands containing 393 genes were detected on 9 different autosomes. Some of these genes were putatively associated with growth performance (AMY1a), stress resistance (THEMIS2,PIK3C2B), meat traits (MBTPS1,DLK1, andEPS8L2), and fat deposition (LANCL2,PPARγ). These findings provide a better understanding of the degree of inbreeding in Wenchang chickens and the hereditary basis of the characteristics shaped under selection. These results are valuable for the future breeding, conservation, and utilization of Wenchang and other chicken breeds.