Analysis of Hg(II) complexed by a soil humic acid (HA) using synchrotron-based X-ray absorption spectroscopy (XAS) revealed the importance of reduced sulfur functional groups (thiol (R-SH) and disulfide (R-SS- R)/disulfane (R-SSH)) in humic substances in the complexation of Hg-(II). A two-coordinate binding environment with one oxygen atom and one sulfur atom at distances of 2.02 and 2.38 Å, respectively, was found in the first coordination shell of Hg(II) complexed by humic acid. Model calculations show that a second coordination sphere could contain one carbon atom and a second sulfur atom at 2.78 and 2.93 Å, respectively. This suggests that in addition to thiol S, disulfide/disulfane S may be involved with the complexation of Hg(II) in soil organic matter. The appearance of carbon atom in the second coordination shell suggests that one O-containing ligand such as carboxyl and phenol ligands rather than H2O molecule is bound to the Hg(II). The involvement of oxygen ligand in addition to the reduced S ligands in the complexation of Hg(II) is due to the low density of reduced S ligands in humic substances. The XAS results from this experiment provided direct molecular level evidence for the preference of reduced S functional groups over oxygen ligands by Hg(II) in the complexation with humic substances.