Thrombolites are build-ups of calcium carbonate that exhibit unlaminated internal structures formed through the interactions of microbial communities and their surrounding environment. These long-lived ecosystems have a fossil record that dates back 2.0 Ga and living examples of these systems serve as important analogs to understand the evolution of microbial communities and the biological mechanisms contributing to calcium carbonate precipitation. Despite recent advances, such as next generation sequencing techniques, we are only beginning to understand the microbial and molecular processes associated with their formation. In this research, a three pronged approach was used to address these communities that included: 1) characterization of the vertical spatial diversity; 2) metagenomic analysis of the dominant Cyanobacteria and associated organisms; and 3) metatranscriptomic analysis to unravel the functional complexity over diel and seasonal cycles. The molecular-based approaches were complemented with microelectrode profiling and in situ stable isotope analysis to further examine the dominant taxa and metabolic activity within the thrombolite-forming communities. Analyses revealed three distinctive zones within the thrombolite-forming mats that exhibited stratified populations of bacteria and archaea. Predictive metagenomics also revealed vertical profiles of metabolic capabilities within the community that had not been previously observed. The carbonate precipitates within the thrombolite-forming mats exhibited isotopic geochemical signatures suggesting that the precipitation within the Bahamian thrombolites is photosynthetically induced. The functional genes were then examined to determine active metabolic pathways over diel and seasonal cycling of the thrombolite. Strong diel and seasonal expression patterns were identified and coincide with changes in environmental conditions, e.g. available daylight, temperature, and oxygen concentrations. These trends include diel cycling of photosynthesis genes, nitrogen fixation and denitrification, methanogenesis and dissimilatory sulfate reduction. This study represents the most extensive molecular analysis to date on an actively accreting microbialite and, together, aims to identify the specific metabolic activity leading to lithification and thrombolite formation.