In this study, ab initio and density functional theory methods have been used to understand the structures and thermodynamic stabilities of complexes formed between l-cysteine and mercury (II) ions in neutral aqueous solution. To better understand the interaction between sulfur and mercury (II) ion, the MP2, B3LYP, M06-2X, and TPSS methods have been used to optimize [HgSHx]2−x, x = 1–4, complexes and compared to benchmark QCISD(T) structures. Furthermore, energies from these same methods are compared to CCSD(T)/CBS(2,3) energies. From these benchmark calculations, the M06-2X method was selected to optimize l-cysteinate-Hg(II) complexes and the MP2 method for estimating complex energies. l-cysteinate-mercury (II) ion complexes are formed primarily by forming a bond between cysteinate sulfur and the mercury ion. Stable complexes of l-cysteinate and mercury can be formed in 1:1, 2:1, 3:1, and 4:1 ratios. Each complex is stabilized further by interaction between carboxylate oxygen and mercury as well as hydrogen bonding among complex cysteinate ligands. The results indicate that at high cysteinate to Hg(II) ratios high-coordinate complexes can be present but at lower ratios the 2:1 complex should be dominant. © 2013 Wiley Periodicals, Inc.