Laser desorption/ionization (LDI) was investigated as an ionization method for Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) studies of natural organic matter (NOM). Using International Humic Substances Society standards, Suwannee River fulvic acid (SRFA) and Suwannee River natural organic matter (SRNOM), LDI was found to ionize a very similar set of compounds (>90% of molecular formulas identity) to the matrix assisted laser desorption/ionization (MALDI), while producing higher quality spectra. A comparison of electrospray ionization (ESI) and LDI spectra showed that different types of compounds are ionized by these methods with only 9.9% of molecular formulas common to both. The compounds ionized by LDI/MALDI belong to low oxygen classes (maximum number of species for O7-O9), while ESI compounds belong to higher oxygen classes (maximum number of species for O14-O16). Compounds ionized by LDI can be classified as aliphatic, aromatic, and condensed aromatics in approximately equal measure, while aliphatic compounds dominated the ESI spectra of SRFA. In order to maximize the coverage of molecular species, LDI, as a particularly convenient and readily deployable ionization method, should be used routinely in combination with other ionization methods, such as ESI, for FTICR MS studies of NOM.