Concentrations and compositions of samples treated with protease inhibitor (PI) were similar to untreated controls over time, indicating that PI alone did not stop bacterial activity. For samples treated with HgCl2, 10–20%of the initial organic carbon and nitrogen, PAAs and lipids were lost. DCAAs and DFAAs increased by about the same amount as PAAs decreased, suggesting that dissolution was a major mechanism for loss of particulate organic compounds. Particulate arginine, tyrosine and threonine were slightly enriched, and 16:3, 18:3 and 18:4 fatty acids depleted, in Hg-treated samples. Moreover, Chl-a decreased by a factor of 4 after one month, compared to controls. Simultaneously, a significant amount of Chl-a O-allomer was produced. Although Chl-a allomerization in oceanic sediment trap samples treated with HgCl2 was not as great as in Hg-treated diatom cultures, we recommend summing Chl-a and the allomer peak areas to avoid underestimating Chl-a concentrations in natural samples, or reporting the allomer separately. HgCl2 is an excellent agent for preventing microbial decomposition of marine particulate materials in both field and experimental use, but the changes in composition it causes must be considered in interpreting analytical results.