The study of microbial mats in extreme environments is of high scientific interest from geological, ecological, and geomicrobiological aspects. These mats represent multilayer bio-structures where each taxonomic group dominates a specific vertical layering distribution resulting from its growth and metabolic activity. In the present study, microbial mats in a hot spring environment from Aedipsos (Euboea Island, Greece) resulting in the creation of thermogenic travertine, were studied through an interdisciplinary approach. The mineralogical composition was determined by optical microscopy, XRD, and SEM-EDS microanalysis, and the identification of Cyanobacteria was made primarily on morphological characteristics. The main mineral phase in the studied samples is calcite and, to a less extent, aragonite, with several trace elements in the mineral-chemistry composition, i.e., up to 1.93 wt. % MgO, up to 0.52 wt. % SrO, up to 0.44 wt. % Na2O, up to 0.17 wt. % K2O, and up to 3.99 wt. % SO3. The dominant facies are lamination and shrubs, which are the most common among the facies of thermogenic travertines of the area. Several layers were identified, (i) a top mainly abiotic layer consisting of calcium carbonate micritic crystals, (ii) a second biotic layer–the Cyanobacteria layer, dominated by the species Leptolyngbya perforans, (iii) a third biotic layer where Leptolyngbya perforans, Chloroflexus and other bacteria occur, and (iv) a deeper abiotic part with several layers where no photosynthetic microorganisms occur. In the upper layers, nineteen (19) species of Cyanobacteria were identified, classified in the orders Chroococcales (37%), Synechococcales (31%), Oscillatoriales (16%), and Spirulinales (6%). Among the identified Cyanobacteria, there are typical thermophilic and limestone substrate species. These Cyanobacteria are found to participate in the biomineralization and biologically-influenced processes, i.e., (i) filamentous Cyanobacteria are trapping calcium carbonate crystals, and diatoms, (ii) extracellular polymeric substances (EPS) create crystal retention lattice contributing to the biomineralization process, and (iii) filamentous sheaths of Cyanobacteria are calcified, resulting in the creation of calcium carbonate tubes.