Thraustochytrids are a group of unicellular marine protists that are noted for their ability to produce high amounts of lipids, especially docosahexaenoic acid (DHA), making them a valuable source for replacing fish oil in aquafeeds. Varying levels of Aurantiochrytrium acetophilum meal (TM) were evaluated as replacement of fish oil in extruded diets for juvenile Atlantic salmon on growth, nutrient apparent digestibility, fatty acid composition in muscle and liver and expression of genes associated with lipid metabolism. Four experimental diets were tested: a control diet without the inclusion of A. acetophilum meal and three experimental diets derived from the control diet, in which fish oil was progressively replaced by the addition of A. acetophilum meal at 2.5% (TM 2.5), 6.5% (TM 6.5) and 12% (TM 12) respectively. After 12 weeks of feeding, the growth, feed conversion, condition factor and survival of the fish were not affected by the inclusion of A. acetophilum in the diet. However, the 12% inclusion significantly decreased the viscerosomatic index of the fish and the digestibility of protein, lipids, ash and energy compared to the other experimental diets. The lipid content and fatty acid profile of the liver and muscle were significantly affected by diet composition. In both tissues, fish fed the TM 12 diet retained the highest levels of DHA. However, it was also observed that EPA concentrations lessened with increasing dietary content of A. acetophilum meal. Finally, the decrease in the expression of Delta 5fad in the fish fed with the TM 6.5 and TM 12 diets showed that fish do not require a higher expression of this desaturase for DHA production, due to the high content of this fatty acid in A. acetophilum meal.