This work is intended to provide a classification of selenium’s minerals based on their chemical composition. Each mineral belongs to a particular mineral system, whose components are the chemical elements required to construct the crystal structure of a mineral (species-defining constituents). The number of components represents the minimum number of independent elements necessary to define the composition of the system. According to their chemical composition, all selenium minerals clearly divided into four groups: native selenium, oxide, selenides, and oxysalts: anhydrous selenites (I) and hydrous selenites and selenates (II). Within each of these groups minerals classified according to the minimum number of components required for their formation. We also present systematized data published on the thermodynamics of minerals, which are unstable (selenides) or formed (selenites) in the weathering zone of sulfide and selenide ores, and determines approaches to the quantitative physicochemical modeling of formation conditions. The Eh–pH diagrams of the Me–Se–H2O systems (where Me =Co, Ni, Fe, Cu, Pb, Zn, Cd, Hg, Ag, Bi, As, Sb Al, and Ca) were calculated and plotted for the average contents of these elements in aqueous weathering solutions in sulfide deposit oxidation zones.