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Background: With the increasing concern for health and nutrition, dietary fat has attracted considerable attention. The composition of fatty acids in the diet is important because they are associated with major diseases including cancers, diabetes, and cardiovascular disease. The fatty acid synthase (FASN) and stearoyl-CoA desaturase (delta-9-desaturase) (SCD) genes affect fatty acid composition (1). The expression of SCD and FASN genes is related to an increase in conjugated linoleic acid (CLA) in dairy products, which benefits human health.The aim of current study was to investigate expression changes of SCD and FASN genes that resulted from crossbreeding the local Baluchi sheep with alien breeds. Methods: We collected tissue samples from the mammary glands of 24 single-born ewes from local Baluchi and synthetic Iran-Black and Arman sheep breeds in the Abbas Abad breeding center. After RNA extraction and cDNA synthesis, real-time PCR was performed with all samples in triplicate. Results:The maximum and minimum expression of SCD and FASN genes was in the local Baluchi sheep and the crossbred Arman sheep, respectively. Conclusions: With the highest SCD and FASN gene expression in local Baluchi sheep and relatively less expression of these genes in synthetic Iran-Black and Arman Sheep breeds, it may be necessary to consider the consequences of crossbreeding local sheep and the fatty acid composition of their dairy products.