Abstract A model is presented for the generation of natural hydrogen from cratonic basement rocks and its migration into the sediments of overlying cratonic basins. It is based on the ‘discovery’ of hydrogen at Bourakebougou in the Taoudeni Basin of Mali. In the ‘Cratonic Greenstone Model’, hydrogen is generated by the serpentinization of olivine-rich, ultramafic rocks contained within Precambrian ‘greenstones’. The model requires a protolith (in greenstones), a supply of water (from groundwater), connecting faults to act as a plumbing system and an indurated sediment cover to retard hydrogen movement. Hydrogen is expelled into the overlying basin sediments, which form the host for hydrogen accumulations. The model describes a continental ‘hydrogen system’, which can form the basis for petroleum-type play-based hydrogen exploration in cratonic settings. Using play elements derived from the model, the Bourakebougou play fairway can be extended across the Taoudeni Basin >700 km northwards of the discovery.