Density functional theory (DFT) calculations have been carried out on the possible degradation/demethylation mechanism of methyl mercury (CH3Hg+) complexes with free cysteine and seleonocysteine. The binding of CH3Hg+ ions with one (seleno)amino acid is thermodynamically favorable. However, the binding with another acid molecule is a highly unfavorable process. The CH3Hg-(seleno)cysteinate then degrades to bis(methylmercuric)sulphide (selenide for the Se-containing complex) which in turn forms dimethyl mercury and HgS/HgSe, the latter being precipitated out as nanoparticles. The dimethyl mercury interacts with water molecules and regenerates the CH3HgOH precursor. The calculated free energies of formation confirm the thermodynamic feasibility of every intermediate step of the degradation cycle and fully support earlier experimental results. In completing the cycle, one unit of mercury precipitates out from two unit: of sources, and thereby Se antagonizes the Hg toxicity. The degradation of CH3Hg-L-cysteinate is thermodynamically more favorable than the formation of CH3Hg-L-cysteinate. The preferred degradation of the CH3Hg-L-cysteinate suggests that another mechanism for CH3Hg to cross the blood-brain barrier should exist.