Deep subsurface microbial communities(1) are believed to be supported by organic matter that was either deposited with the formation sediments or which migrated from the surface along groundwater flowpaths. Investigation has therefore focused on the existence of microorganisms in recently deposited or highly permeable sediments(2,3). Fewer reports have focused on consolidated rocks(4-7). These findings have often been limited by inadequate tracer methodology or non-sterile sampling techniques. Here we present evidence for the presence of spatially discrete microbial communities in Cretaceous rocks and advance a mechanism for the long-term survival of these subterranean communities. Samples were collected using aseptic methods and sensitive tracers(8). Our results indicate that the main energy source for these communities is organic material trapped within shales. Microbial activity in shales appears to be greatly reduced, presumably because of their restrictive pore size(9). However, organic material or its fermentation products could diffuse into adjacent, more permeable sandstones, where microbial activity was much more abundant, This process resulted in the presence of microbial communities at sandstone-shale interfaces. These microorganisms presumably ferment organic matter and carry out sulphate reduction and acetogenesis.