We have revealed early productive disseminated pyrite-arsenopyrite mineralization with invisible gold in tectonic zones and late nest-veinlet gold-polysulfide mineralization with free gold in zones of silicified rocks at the Suzdal’ (Suzdal’skoe), Zherek, and Bol’shevik deposits in eastern Kazakhstan, localized within black shales. Two varieties of arsenopyrite differing in morphology, chemical composition, and gold contents have been established in them: acicular-prismatic and tabular. Gold was determined by a specially elaborated technique ensuring a detection limit of 30 ppm Au. Acicular-prismatic arsenopyrite is the main ore mineral of the early productive stage of mineralization; it has high gold contents (1400–5360 ppm) and a nonstoichiometric composition (S/As = 1.2) and is slightly depleted in Fe. The absence of correlation between the contents of the main arsenopyrite components and gold, and the strongly uneven distribution of gold among the mineral grains, and within a grain point to the presence of invisible gold, as elemental particles deposited together with arsenopyrite. Tabular arsenopyrite is abundant at the Suzdal’ deposit, where gold-polysulfide mineralization and argillization are widespread. It has low gold and high antimony contents and a stoichiometric composition. Visible gold usually grows over tabular arsenopyrite. The isotopic composition of sulfur of acicular-prismatic arsenopyrite and globular-crystalline pyrite, formed at the early mineralization stages, is characterized by δ34S = 0.0 to –3.3‰ and evidences a mantle source of sulfur with a partial borrowing of crustal sulfur. The tabular arsenopyrite and other sulfides of the second productive mineralization show a lighter isotopic composition of sulfur (δ34S = –7.7 to –10.2‰), which is due to sulfur fractionation under high oxygen fugacity at the late ore deposition stage. The coexistence of two sets of arsenopyrite of different morphologic varieties and compositions at the deposit points to a long ore deposition, the coexistence of mineralization formed at different stages, and the evolution of physicochemical parameters.