In this study, we evaluated whether oil extracted from the marine microbe, <i>Schizochytrium</i> sp. (strain T18), with high levels of docosahexaenoic acid (DHA), could replace fish oil (FO) in diets for rainbow trout (<i>Oncorhynchus mykiss</i>). Three experimental diets were tested: (1) a control diet with fish oil (FO diet), (2) a microbial oil (MO) diet with a blend of camelina oil (CO) referred to as MO/CO diet, and (3) a MO diet (at a higher inclusion level). Rainbow trout (18.8 ± 2.9 g fish⁻¹ initial weight ± SD) were fed for 8 weeks and evaluated for growth performance, fatty acid content and transcript expression of lipid-related genes in liver and muscle. There were no differences in growth performance measurements among treatments. In liver and muscle, eicosapentaenoic acid (EPA) was highest in trout fed the FO diet compared to the MO/CO and MO diets. Liver DHA was highest in trout fed the MO/CO diet compared to the FO and MO diets. Muscle DHA was highest in trout fed the MO and MO/CO diets compared to the FO diet. In trout fed the MO/CO diet, compared to the MO diet, <i>fadsd6b</i> was higher in both liver and muscle. In trout fed the FO or MO/CO diets, compared to the MO diet, <i>cox1a</i> was higher in both liver and muscle, <i>cpt1b1a</i> was higher in liver and <i>cpt1a1a</i>, <i>cpt1a1b</i> and <i>cpt1a2a</i> were higher in muscle. <i>Schizochytrium</i> sp. (T18) oil was an effective source of DHA for rainbow trout.