A comprehensive study of authigenic carbonates and associated fauna in Late Albian organic-rich, deep-water deposits (the Black Flysch Group) reveals that carbonate precipitation was a by-product of the anaerobic oxidation of hydrocarbon-rich hydrothermal fluids. The authigenic carbonates are exposed along the Kardala and Alkolea sea cliffs in the western Pyrenees. The two vent carbonates occur 1 km apart adjacent to the synsedimentary, right-reverse Mutriku fault, but in contrasting structural domains: the Kardala carbonates occur on a structural ridge (hangingwall) and the Alkolea carbonates are positioned at the base of an erosional scarp (folded downward footwall). The similarity in pattern of the carbonate phases and complex paragenetic events for both vent precipitates implies that hydrothermal fluid generation processes and pore-water evolution during early and late diagenesis were similar. Nevertheless, a comparison of the geochemistry, fossil fauna and morphology of carbonate structures of both precipitates suggests that the vented hydrocarbon type, flow intensity and temperature of hydrothermal fluids were different. At the Kardala vent, intense focused flow of hot (up to 109 °C), oil-rich fluids were generated, allowing the development of a relatively abundant chemosynthesis-based fauna. In contrast, at the Alkolea vent, diffuse flows of warm, thermogenic methane-rich fluids were expelled to the sea floor and no chemosynthetic fauna developed. These differences are related to the contrasting structural setting of each locality. Similar δ13Corg values for both pyrobitumen-fills and host unit organic matter suggest that the hydrocarbon source was the Black Flysch Group. Contact alteration of these organic-rich sediments by syndepositional hydrothermal fluids generated hydrothermal petroleum (oil and gas hydrocarbons) which probably migrated updip to the sea floor by contemporary compression tectonics.