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Some well-developed microbial mats have calcified structures called microbialites in Storr’s Lake, a hypersaline lake on the east coast of San Salvador Island, Bahamas. Many of theses microbialites are laminated, and therefore classified as stromatolites. This study focuses on a small stromatolitic knob collected from the bottom of Storr’s Lake, whose mineralogy is dominated by aragonite and high-Mg calcite. These two minerals appear to dominate different layers that are classified by the depth below the top surface of samples. This study concentrates on mapping and finding the distribution of these two minerals. Titan-Yellow staining colorfully distinguished mineralogical spatial distribution in stromatolites, while a higher resolution of aragonite and high-Mg calcite distribution was accomplished by using a Scanning Electron Microscope. The stromatolitic intervals include oriented, wavy to parallel carbonate and organic-rich laminae from Titan-Yellow stainning results, as well as 1 mm diameter spherules with laminae of aragonite. Botryoidal aragonite is either discontinuous (distinct botryoids) or forms more continuous laminae (coalesced botryoids). This project can be used to inform future studies of fine-grained stromatolites in the fossil record, and discussion about controls and formation procedure on the mineralogical compositions.