The relationship between the respiration and the presence and utilization of endogenous and exogenous substrates was studied in the non-filamentous obligately marine fungus Thraustochytrium aureum. Using isotopic and manometric methods, it was shown that almost all exogenous glucose is assimilated, whilst almost all the oxygen consumption in the presence of exogenous glucose was due to oxidation of endogenous reserves. In contrast, exogenous glutamate, which cannot serve as the sole carbon source for growth, inhibits respiration of endogenous materials, and is itself rapidly oxidized. The uncoupler 2,4-dinitrophenol stimulates the oxidation of endogenous reserves without affecting the uptake and use of exogenous glucose. These data strongly support the idea of physiologic compartmentation in this organism.