Diverse metabolic reactions occur in marine sediments that directly affect the sedimentary environment and alter the physical and chemical state. In turn, the sedimentary environment affects microbial distributions. However, microbe-mineral interactions are poorly understood in marine sediments and as such the knowledge about the consequences of microbial metabolisms on the sediment geochemistry is lacking. This lack of knowledge is in part because observations from sedimentary environments are typically based on bulk community and geochemical analysis, where several grams of sediment are mixed for the analysis. The bulk analysis of microbial distributions and mineralogy does not reflect a scale that is relevant to the heterogeneous nature of sediment for microbial communities. Furthermore, direct observations of microbial distributions and associations to minerals have not been described, until now. A fluorescence in-situ hybridization technique that uses gold nanoparticles (Gold-FISH) was adapted for marine sediments. The gold nanoparticles allowed for cell identification using a scanning electron microscope equipped with energy dispersive spectroscopy (EDS), which also allowed for identification of surrounding elements. Using Gold-FISH on sediment samples from the Dorado outcrop typically found bacterial cells in clusters or micro-colonies attached onto shells. This information aids in the understanding of the micron distribution of microbes in marine sediments.