Schizochytrium sp. (Sc) is a promising nutritious and sustainable source of polyunsaturated fatty acids (PUFAs) in aquafeeds for carnivorous fish. This study investigated the apparent digestibility coefficients (ADCs) of PUFAs, along with macronutrients, other major fatty acids (FAs) and gross energy of Sc whole cells when included in diets for Atlantic salmon (Salmo salar). Thirty fish (27.9 +/- 1 g) were randomly allocated to eight-120 L tanks and fed a reference or test (70% reference diet and 30% Sc biomass) diet. Over three weeks fish feces were collected by sedimentation using fecal collection columns and analyzed for digestible dry matter, gross energy, macronutrients, and FAs. ADCs of protein, lipid, and gross energy of Sc were 93.9%, 67.1% and 70% respectively. Major FAs in the Sc ingredient were palmitic acid (44.7%% FAME), docosahexaenoic acid (33.2% FAME) and docosapentaenoic acid (10.1% FAME). SFAs and PUFAs in the test diet were 15% and 7.4% higher than the reference diet, which was reflective of Sc's FA composition. Dry matter, total lipid, gross energy and SFAs were significantly (p < 0.001) more digestible in the reference diet. PUFAs and DHA were well digested (>95%) in both diets but significantly (p = 0.038 and p < 0.001, respectively) more digestible in the test diet. This study shows that whole cell Sc offers a source of highly digestible (98%) PUFAs and protein with no need for oil extraction or cell disruption.