High-grade gold and uranium mineralization in the Witwatersrand basin is intimately associated with pyrobitumen, implying that hydrocarbons may have played a role in the genesis of these ores. The nature of the pyrobitumen in the Carbon Leader Reef was therefore investigated to determine if hydrocarbons were essential to the ore-forming process. The relative proportions of trace elements in pyrobitumen seams and nodules are, in large part, similar to those of organic-rich shales located within the sedimentary succession. This indicates a strong genetic relationship between the pyrobitumen and the shales. A network of veins and veinlets filled with pyrobitumen, and the occurrence of oil inclusions in detrital and authigenic quartz grains, provide compelling evidence that the pyrobitumen was derived from a mobile (liquid hydrocarbon) precursor that circulated in the Carbon Leader Reef. Uranium, Au, Sb, Pb, Ag, Te, Th, Bi, Se and W are enriched relative to their concentrations in the shales. This is particularly the case for U and Au. The pervasive and relatively homogeneous distribution of the uranium is consistent with the presence of ubiquitous, submicroscopic uraninite in the pyrobitumen documented in an earlier study. In contrast, the distribution of the gold is heterogeneous, indicating the presence of irregularly distributed gold micrograins. These grains are concentrated mainly in the interstices between pyrobitumen nodules. Secondary minerals, such as brannerite, monazite-(Ce) and galena, are also concentrated in these interstices. On the basis of this study, we propose that intrabasinal shale units of the Witwatersrand Supergroup were the source for the pyrobitumen in the Carbon Leader Reef. These shales produced and released liquid hydrocarbons during the burial of the sedimentary succession. Phyllosilicates enriched in trace metals were transferred from the shales into the newly produced liquid hydrocarbons and were transported stratigraphically upward by the latter into the Carbon Leader Reef. During migration, the liquid hydrocarbons dissolved detrital uraninite present in the basin, adding to the uranium budget. The liquid hydrocarbons were converted into pyrobitumen in response to further burial, and precipitated uraninite nanocrystals. Post-depositional, hydrothermal fluids interacted with the hydrocarbons and deposited gold by reduction on hydrocarbon surfaces. The interaction of these fluids with the hydrocarbons may have released U, Th, REE, Pb and Ti from the hydrocarbons and triggered the formation of secondary brannerite, monazite-(Ce) and galena. The results of this study provide convincing evidence that the hydrocarbon liquids that formed the pyrobitumen seams in the Carbon Leader Reef played an essential role in the remobilization and redeposition of uranium and gold, respectively, in the Witwatersrand Supergroup. •Pyrobitumen represents the residues of liquid hydrocarbons produced in intra-basinal shale units.•Uranium is ubiquitous in pyrobitumen seams and is mainly present as invisible uraninite.•Hydrocarbon liquids dissolved detrital uraninite during their migration through the Witwatersrand basin.•Gold was precipitated from hydrothermal fluids by reduction on hydrocarbon surfaces•Hydrothermal leaching of hydrocarbons led to the formation of secondary minerals.