The formation of two types of animal pigments, brown to black eumelanin and yellow to reddish yellow pheomelanin, occurs primarily through a branched reaction in melanogenesis. This branching takes place by competing reactions that involve dopaquinone (DQ), which is a key to understand the melanocyte-related tissue reactions. In the presence of L-cysteine, DQ immediately binds to the -SH group, initiating the pheomelanin production. L-cysteine prefers to bond with aromatic carbons adjacent to the carbonyl carbons, namely C5 and C2. On the other hand, the competitive cyclization of DQ, which is the initial step of eumelanin production, occurs at the C6 atom. Such remarkable contrast necessitates an atomic-scale understanding of the binding mechanism between L-cysteine and DQ. Using density functional theory-based first principles calculations, we investigated the binding of L-cysteine thiolate (Cys-S-) to DQ.