Hydrothermal synthesis experiments were performed in order to quantify the states of Au and As in pyrite and marcasite. The experiments were performed at 350 °C/500 bar and 490 °C/1000 bar (pyrite–pyrrhotite buffer, C(NaCl) = 15 and 35 wt.%). The synthesis products were studied by EPMA, LA-ICP-MS, and EBSD. The EPMA was applied for simultaneous determinations of Au, As, Fe, and S, with a Au detection limit of 45–48 ppm (3σ). The analyses were performed along profiles across zonal grains. The concentrations of As and Au up to 5 wt.% and 8000 ppm, respectively, were determined in pyrite and up to 6 wt.% and 1300 ppm in marcasite. In pyrite, the Au concentration decreases with fluid salinity and temperature increases. Strong positive Au–As correlation and strong negative Au–Fe and As–S correlation were identified in pyrite. Comparison of the correlations with theoretical lines implies Au–As clustering. The cluster stoichiometry is inferred to be [AuAs10]. Most probably, As in pyrite presents in the form of clusters and in the As→S solid solution. Incorporation of Au in As-rich pyrite can be controlled by the reductive deposition mechanism. In marcasite, the concentrations of Au are not correlated with the As content. The [AuAs10] clusters enrich the {210}, {113}, and {111} pyrite faces, where the former exhibits the highest affinity to Au and As. The affinity of {110} and {100} forms to Au and As is lower. Implication of the experimental results to data for natural auriferous pyrite shows that the increase of Au content at C(As) > 0.5–1 wt.% is caused by the incorporation of the Au-As clusters, but not because of the formation of Au→Fe solid solution. Therefore, the concentration of “invisible” gold in pyrite is dictated solely by the hydrothermal fluid chemistry and subsequent ore transformations.