Authigenic aragonite preserves a carbon isotopic record of heterotrophic microbial influences on dissolved inorganic carbon (DIC) in microenvironments within shallow subtidal stromatolites from Highborne Cay, Bahamas. A greater amount of aragonite precipitates when and where respiration, rather than photosynthesis, influences local DIC, which is consistent with sulfate reduction promoting carbonate precipitation and calcium release during decay of exopolymeric substances. Thus, heterotrophs play a more direct role than phototrophs in stromatolite lithification. Cyanobacteria are spatially associated with aragonite containing heterotrophic isotopic signatures. Hence, the absence of an autotrophic isotopic signature in the rock record does not imply the absence of photosynthetic organisms.