Microalgae could be an important source of biomass for biofuels due to their fast growth rate, ability to be grown in brackish water, and for accumulating large percentages of lipids and starch. Previous studies have shown that limited nitrogen conditions induce a stress response in algae that results in increased lipid production. Since nitrogen may play a key role in the cell wall structure of microalgae, cell wall structures may be altered due to the environmental changes associated with nitrogen. Additionally, use of the cell wall could be affected by protein content, which can inhibit digestion and fermentation. This study investigated the changes in the cell wall of algae under nitrogen-limited conditions. The microalgae were grown in normal nitrogen levels, then removed and washed of their growth media, and grown further in low nitrogen conditions. After growth, the algae were lyophilized, defatted, and enzymatically digested for the removal of starch. The remaining biomass was derivatized by the Trimethylsilyl Methylglycosides (TMS) method and analyzed using quadrupole gas chromatography/mass spectrometry (GC/MS). TMS derivatization allows for complete mass balance and identification of novel sugars since neutral, amino, and acidic sugars can be detected. Results will be used to understand the ramifications of nitrogen stress on the cell wall and potential uses for the cell wall.