Buried carbonate reefs are favoured hydrocarbon prospecting targets, mainly due to their high porosity and potential for containing large quantities of petroleum. The question of the true relationship between reef structure and the internally trapped fluids (hydrocarbons) is here raised as one of cause - and effect. In other words, which came first, the hydrocarbons or the carbonate reef itself?Modern bioherms and seabed carbonate reefs in, amongst other locations, the North Sea and the Gulf of Mexico, are shown to form in close association with active hydrocarbon seepages. Mainly based on results from ecological studies at deep-ocean vent communities, a new model for carbonate reef formation is promoted: that such reefs form at locations containing high concentrations of bacteria and other microorganisms suspended in the water column as a result of seeping fluids (solutions and gases) that provide some of the energy basis and carbon source for ecosystems independently of photosynthesis. Therefore, on burial and effective sealing (‘capping’), these carbonate reefs become hydrocarbon reservoirs, trapping and accumulating the very minerals on which they - in the first place - were dependent.