Proteins and amino acids of the diatom Thalassiosira fluviatilis and the cyanobacterium Synechococcus sp. were quantified during an aerobic decomposition period of 61 days. We developed a micro-method for the extraction and analysis of proteins and amino acids in particulate material. The bicinchoninic acid assay (BCA) and a ribulose-l,5-diphosphate carboxylase standard was used to estimate total protein. Protein degradation did not follow a simple exponential, first order decay due to the presence of bacterial communities. Instead, there were oscillations, which correlated with changes in bacterial metabolism and population numbers. We estimated 40-50 % protein in the cyanobacterium. The diatom appeared to have significantly more protein but we determined that this was an overestimation. Chitin, a major component of diatom cell walls which precipitates with proteins, was found to enhance the BCA reaction. In order to correct for chitin, an assay was performed using a lectin that binds specifically to chitin. For the diatom, every amino acid seems to degrade at the same rate with the exception of arginine. Arginine amounts actually increase in the same time frame as when the bacterial populations increase. For the cyanobacterium, most of the percent composition of amino acids stays the same with the exception of arginine, glycine, serine, and tryptophan. All of these four amino acids also increase around day 10.