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Simple Summary Milk fatty acid composition and gene expression in the mammary gland were evaluated in dairy ewes supplemented with linseed. The linseed supplementation improves the health and nutrition quality properties of dairy milk, besides affecting the expression of gene networks related to energy balance, RNA binding, circadian rhythm, and nutrient metabolism. This molecular knowledge on the physiology of the mammary gland might provide the basis for more detailed functional studies for future research. Abstract Several dietary strategies were adopted to reduce saturated fatty acids and increase beneficial fatty acids (FA) for human health. Few studies are available about the pathways/genes involved in these processes. Illumina RNA-sequencing was used to investigate changes in the ovine mammary gland transcriptome following supplemental feeding with 20% extruded linseed. Comisana ewes in mid-lactation were fed a control diet for 28 days (control period) followed by supplementation with 20% DM of linseed panel for 28 days (treatment period). Milk production was decreased by 30.46% with linseed supplementation. Moreover, a significant reduction in fat, protein and lactose secretion was also observed. Several unsaturated FAs were increased while short and medium chain saturated FAs were decreased by linseed treatment. Around four thousand (1795 up- and 2133 down-regulated) genes were significantly differentially regulated by linseed supplementation. The main pathways affected by linseed supplementation were those involved in the energy balance of the mammary gland. Principally, the mammary gland of fed linseed sheep showed a reduced abundance of transcripts related to the synthesis of lipids and carbohydrates and oxidative phosphorylation. Our study suggests that the observed decrease in milk saturated FA was correlated to down-regulation of genes in the lipid synthesis and lipid metabolism pathways.