The presence of microbialites in the hypersaline lagoons of Rio de Janeiro is especially important in the study of recent analogs of carbonate rocks with microbial origins, mostly after the discovery of giant petroleum reservoirs in the Brazilian pre-salt section and their similarities with stromatolites from Lagoa Salgada (Rio de Janeiro State). Many studies have been conducted to analyze the biology, geochemistry, mineralogy, and geomicrobiology of these microbialites. This paper, however, focuses on the petrography, sedimentology, and geochemistry of recent and superficial microbial mats from Lagoa Vermelha to understand the interaction of carbonate and siliciclastic grains with an organic matrix and discuss their similarities and differences with pre-salt rocks. A sedimentologic description was performed to understand the sediment dynamics in microbial mats. A petrographic description involved the characterization of components and textures in microscale. Furthermore, geochemical analyses were performed using scanning electron microscopy and X-ray diffraction for detailed mineralogical characterization. This multitechnique study showed the lamellar and cracked texture of the matrix being displaced by biologically induced carbonate growth and siliciclastic grains. In addition, chemical analysis showed the concentration of magnesium and silica in the matrix, with the absence of Mg-clay minerals. Even though the studied microbial mats present relevant similarities with some pre-salt facies, a microbially dominated genesis for the pre-salt limestones cannot be supported by the studied data.