The typomorphic features of pyrite of the Sukhoi Log deposit were studied by a set of volumetric and surface methods: electron probe microanalysis, scanning electron and probe microscopy, powder X-ray diffraction, X-ray photoelectron and Auger electron spectroscopy, atomic-absorption spectrometry in the SSADSC (method of statistical sample of analytical data for single crystals) version, and atomic-emission spectrometry. Pyrite from the Sukhoi Log deposit has the following distinctive features: permanent presence of sulfite ion, which often dominates over other surface sulfur anions; weakly determined size dependence of the content of uniformly distributed Au owing to the presence of an internal concentrator of gold—dispersed carbonaceous material—in pyrite from ore zones; cell sculptures of the crystal faces, which appeared owing to the nanofragmentation of the growth surface; micro- and nanoinclusions of carbonaceous phases within crystals, associated with defects in their structure; and thin films enriched in O and C on the surface of and within the crystals. It has been shown that gold–sulfide mineralization at the Sukhoi Log deposit formed in a single ore-generating hydrothermal system, in which gold, sulfur, and carbon belonged to a microparagenesis. Some features (composition of surface, characteristics of submicroscopic structure, and elemental composition) evidence that the conditions of crystallization of pyrite in inter-ore space were different from the conditions of its genesis in the ore zones, which suggests the presence of at least two genetic types of pyrite. Carbonaceous micro- and nanoparticles and O- and C-containing films can favor an increase in the adsorption of gold from cyanide solutions on pyrite. To reduce this effect during gold recovery, a technique for surface modification should be elaborated. The ways for solving the most complicated problems dealt with the source of noble metals (NM) and the ore specialization of the deposit have been outlined. For this purpose, a detailed analysis of the main ore minerals for trace-element speciation is required. In the case of the magmatic source of NM, correlation between the contents of Au and PGE structural forms should exist. On the other hand, there is no correlation between the structural forms of Au or Pt and elements whose contents in fluid are determined by the host rock rather than the magmatic source.