ABSTRACT. The direction of production for indigenous chicken breeds is currently unknown and this knowledge, combined with the development of chicken genome-wide association studies, led us to investigate differences in specific loci between broiler and layer chicken using bioinformatic methods. In addition, we analyzed the distribution of these seven identified loci in four Chinese indigenous chicken breeds, Caoke chicken, Jiuyuan chicken, Sichuan mountain chicken, and Tibetan chicken, using DNA direct sequencing methods, and analyzed the data using bioinformatic methods. Based on the results, we suggest that Caoke chicken could be developed for meat production, while Jiuyuan chicken could be developed for egg production. As Sichuan mountain chicken and Tibetan chicken exhibited large polymorphisms, these breeds could be improved by changing their living environment.