The complexation of U(VI) by organic P-containing ligands in humic substances (HS) is an important issue of uranyl mobility in soil. We have investigated the complexation of uranyl by a model ligand for aromatic phosphorus functionalities in HS, phenylphosphonic acid, by using ultrahigh resolution electrospray ionization-mass spectrometry (ESI-MS). The high sensitivity permitted to investigate the complexation of trace level uranyl and to explore directly in the native aqueous solutions the nature of the uranyl-phenylphosphonate complexes. Positive identification of the complexes coexisting in solutions with low pH and varying ligand-to-metal ratio was achieved thanks to the high resolving power, high mass accuracy, and reliability of ion abundance of the technique. The positively charged and neutral uranyl species were detected simultaneously on negative ion mass spectra, evidencing formation of three types of U(VI)-phenylphosphonate complexes. Two complexes with a metal-to-ligand stoichiometry of 1:1 (in the monoprotonated and nonprotonated forms) existed in solutions at pH 3-5, and a 1:2 complex was additionally formed at relatively high ligand-to-metal ratio. A strategy based on the use of uranyl-phosphate solution complexes as internal standards was developed to determine from the ESI(-)MS results the stability constants of the complexes, which were calculated to be log K111 = 3.4 ± 0.2 for UO2(HPhPO3)(+), log K101 = 7.1 ± 0.1 for UO2PhPO3, and log K112 = 7.2 ± 0.2 for UO2(HPhPO3)2. The speciation model presented here suggests that organic P existing at low concentration in HS is involved significantly in binding by humic and fulvic acids of trace level uranyl in soil.