Using the 15N stable isotope technique, nitrogen (N) assimilation of Artemia was determined in feeding regimes where the two yeast strains wild-type (WT) and its mutant mnn9 were gradually replaced by HT3 or HT6, or where the bacterial strains were gradually replaced by each yeast strain. A trypsin assay was performed on Artemia fed the various replacement feeding regimes, in order to detect the effect of the presence of bacteria or of the yeasts on the protein digestive response in Artemia. HT6 fed Artemia showed a higher N assimilation than when using HT3, suggesting a better food value of HT6 for Artemia. The assimilation of nitrogen from bacteria was related to the presence of yeast strains. In the HT3 fed Artemia group, the presence of WT yeast showed higher N assimilation from HT3 than the presence of mnn9, suggesting an enhanced utilization of poor quality HT3 in the presence of WT yeast. When using the higher quality HT6 on the other hand, mnn9 acted in a very similar manner. This is the first observation where mnn9 improves the N assimilation from any bacteria. When N assimilation from yeast strains was tested in the presence of bacteria, both bacterial strains HT6 and HT3 showed a clear enhancement in utilization of N from mnn9, probably by providing exogenous enzymes, highlighting the additional importance of these strains of bacteria for Artemia in utilizing yeast. A significant reduction (p < 0.05) of trypsin activity was observed in Artemia fed HT3 alone, as compared to all other feeding treatments, confirming the lower suitability of the HT3 isolate for sole feeding of Artemia. We conclude that HT6, being a better N source for Artemia, also favors the utilization of N derived from yeast in the food.