Organic matter (OM) and rocks of the upper member of the Mesoproterozoic Malgin Formation in the southeastern Siberian Platform have been studied by modern research methods. Analysis has revealed homologous series of alkanes, tricyclanes, and hopanes in the bitumens. Leiosphaeridia crassa, L. minutissima, cf. Leiosphaeridia tenuissima, cf. Glomovertella, and Oscillatoriopsis sp. have been identified among the rare microfossils preserved in mudstones. Geochemical, lithological, and paleontological studies have shown that bacterial microcommunities and, to a lesser extent, eukaryotic microorganisms were the main source of OM. Based on results of sedimentological analysis and study of biomarkers, the depositional environment has been reconstructed. A model for the accumulation of black shales and carbonate rocks of the Malgin Formation is considered. The hypothesis that the highly carbonaceous rocks formed in uncompensated depressions of shallow epicontinental marine suboxidation environments is substantiated. The petroleum potential and degree of OM catagenesis of the Malgin Formation rocks are evaluated. Pyrolysis, bitumen analysis, and hydrocarbon composition study have revealed autochthonous and parautochthonous bitumens in the oil shales, mudstones, and carbonate rocks. The obtained data show that the Malgin Formation rocks might have participated in petroleum generation in the Uchur–Maya region.