Technical Abstract: The chemical properties of organic matter affect important soil processes such as speciation, solubilization, and transport of plant nutrients and metals. This work uses ultrahigh resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry to determine the molecular composition of three organic matter fractions of soils and aqueous extracts of crop biomass. van Krevelen plots were compared, allowing the changes in organic matter with increasing humification to be tracked. Aqueous plant biomass extracts contain a diverse mixture of lipids, proteins, and lignins. Soil aqueous extracts were marked by increases in lignin and carbohydrates and a decrease in the proteins as compared to the plant extract. Refractory humic acid fractions were marked by a decrease in lignin and increases in the lipid and condensed aromatic components. The multivariate indicator species analysis was used to identify marker components of the four organic matter types investigated. The plant extract group had 590 marker components, compared to 204 for soil aqueous extracts, 76 for mobile humic acids, and 250 for calcium humic acids. This study demonstrates that ultrahigh resolution mass spectrometry and multivariate statistical methods can be used to identify marker components to gain a molecular-scale description and understanding of carbon dynamics.