Delta-6 fatty acid desaturases are rate-limiting desaturases involved in metabolic processes of fatty acids, and they are encoded by the FADS2 gene. In the current study, an F2 resource population of Gushi chickens crossed with Anak broilers was used to investigate the genetic effects of the chicken FADS2. Two adjacent single nucleotide polymorphisms (SNPs) (g.4290C>G and g.4291C>A) were identified in the transcriptional regulatory region of the FADS2 gene by means of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and created restriction site-PCR-RFLP. Associations between the two SNPs with chicken fatty acid contents and growth traits were determined using linkage disequilibrium, haplotype construction, and association analysis. The two SNPs and their haplotype combinations were significantly associated with linoleic acid (C18:2), α-linolenic acid (C18:3), arachidonic acid (C20:4), body weight (BW)2, BW4, BW6, shank girth (SG)4, and breast bone length 4 (P FADS2 gene affected the content of essential fatty acid in muscle, and played a role in the early-stage growth rate of chickens.