Determination of apparent digestibility coefficients (ADC) of ingredients has a central importance in formulation of aquaculture diets. Heterotrophic and phototrophic grown microalgae are considered as one of the best eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) as well as protein alternatives for fish oil and fish meal (FM) to sustain further growth in aquaculture production. This study aimed to determine nutrient and fatty acid ADCs of microbial materials including Nannochloropsis oceanica, Phaeodactylum tricornutum and two thraustochytrid strains (T29 and T66) with comparison to commonly used ingredients such as two batches of FMs, poultry-by product meal (PBM), soybean meal (SBM), corn gluten meal (CGM), wheat gluten meal (WGM) and whole wheat flour (WF) in rainbow trout, Oncorhynchus mykiss. Each ingredient was tested using Cr2O3 as an indigestible marker in triplicated cylindro-conical tanks for 2 weeks. Protein ADCs of microbial ingredients ranged between 77.6% in T66 and 84.4% in P. tricornutum and were close to those of FMs and PBM. N. oceanica had generally significantly lower lipid and fatty acid ADCs than those of P. tricornutum, thraustochytrids and the conventional feed ingredients probably due to their thick cell walls. Between the thraustochytrids strains, the T66 appeared to have slightly lower lipid, energy, organic matter, saturated, monounsaturated, long chain n-6 and long chain n-3 fatty acid ADCs than T29. P. tricornutum showed comparable nutrient ADC values to the two FMs used in the study. The results suggest that even if the microbial ingredients were used at 30% in reference diet without exposition to a pretreatment process, they can be utilized at acceptable rates by rainbow trout.