The aim of this study was to determine the variants of the thio esterase (TE) beta-ketoacyl reductase (KR) domains of the Fatty Acid Synthase (FASN) gene, in the East Anatolian Red (EAR) and South Anatolian Red (SAR) cattle breeds. It has been suggested that the FASN gene is effective on fatty acid composition of meat in cattle. In this study, the genotype and allele frequencies of g.17924 A>G, g.18440 G>A and g.16024 G>A, g.16039 T>C in TB and KR domains, respectively, were detected by using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) method. The g.18663 T>C polymorphism of the TB domain was determined by direct sequencing. The GO genotype of the g.17924 A>G polymorphism, which affects unsaturated fatty acid composition positively, has a high frequency in EAR and SAR breeds. The frequencies of the two haplotypes g.16024 G>A and g.16039 T>C in the KR domain were found to be significantly high in both breeds. These haplotypes also have positive effects on unsaturated fatty acid composition. The AA genotype of the g. 18440 G>A polymorphism, which is suggested to be absent in Bos taurus breeds, was detected in SAR and EAR breeds with frequencies close to those in Bos indicus breeds. In conclusion, we suggest that SAR and EAR cattle breeds have an advantage in terms of genotype and haplotype distribution of the polymorphisms in TE and KR domains of the FASN gene. Additionally g.18440 G>A polymorphism might be a potential marker for breed discrimination.