The feather, a highly keratinized tissue with variations in the shape, distribution, pigmentation, and structure, is an attractive topic in developmental and evolutionary biology (Boer et al., 2017). One phenotype noted by Darwin (Darwin, 1868), frizzle, consists of feather rachis and barbs curling outwards. It was previously reported that a 69-bp deletion in KRT6A (formerly named as KRT75 in the original paper; see Supplementary Materials and methods for details) was responsible for frizzle in chicken (Ng et al., 2012). Nevertheless, a recent screening of KRT6A in the Qilin chicken, a frizzle breed from Southern China (Supplementary Materials and methods, and Figures S1 and S2), failed to detect the 69-bp deletion (Tao et al., 2015). This raises a possibility that there is an independent genetic mechanism determining frizzle in Qilin chicken. To dissect this issue, we adopt a comparative population genomic strategy to investigate the genetic basis underlying frizzle in Qilin chickens. This strategy has been shown efficient in studying the phenotypic evolution in chicken (Wang et al., 2016, 2017).