The objective of this study was to determine gene expression patterns in the muscle tissue of finishing heifers fed diets supplemented with DHA-rich algae. Angus-cross heifers (n = 285; 453 ± 24 kg initial BW) were randomly assigned to one of 4 treatments: control (CON) or 50, 100, or 150 g/d of DHA-rich microalgae (ALG, Schizochytrium limacinum CCAP 4087/2, Alltech Inc., Nicholasville, KY). Muscle samples (n = 9 per treatment) were obtained via biopsy from the Longissimus dorsi and gene expression was analyzed using the Affymetrix Bovine Gene 1.0 ST Array. Relative to the CON, a total of 2047 differentially expressed genes (DEG, 919 upregulated and 1128 downregulated), 711 genes (343 upregulated and 368 downregulated), 956 genes (440 upregulated and 516 downregulated), were differentially expressed in the 50, 100 and 150 g/d treatment groups, respectively. In the 50-g treatment group, DEG encoding enzymes involved in the synthesis of n-3 PUFA included ELOVL2 (−1.15 fold), ACOX1 (1.19 fold) and SCP2 (1.22 fold). These genes were unchanged in the 100-g and 150-g treatment groups. Biological functions commonly enriched in all 3 treatment groups included cellular development and lipid metabolism. DEG involved in free radical scavenging, including catalase (1.16 fold), superoxide dismutase (1.18 fold) and peroxiredoxin (1.14 fold) were increased in the 150-g treatment group, supporting previous findings that markers of lipid oxidation in muscle were increased in this group. Overall, these results suggest that supplementing finishing heifer diets with ALG alters the expression of genes involved in lipid metabolism and lipid accumulation in muscle tissue, and that these alterations are dose dependent.