Abstract The action of the microorganisms upon the integrity of the constructing material is termed Biodeterioration, concrete resistance to the action of the microorganisms is considered an indirect measurement of its durability and could be used as a marker of the integrity of the structure. In Colombia, the studies considering this parameter are rare. The objective of this study was to isolate and characterize the microbial communities present in areas with evident deterioration in the selected buildings. To accomplish this, isolation, culturing and molecular identification of the isolates was performed. Results showed that Cladosporium spp, Aspergillus spp, Mucor spp, Penicillium spp, Penicillium spp, Rhizopus spp, Fusarium spp, Geotrichum spp, and bacterial genera such as Bacillus spp and Amphibacillus spp, coexist within the biofilms sampled. This study is a description and a starting point to deepen the characterization of these communities and to understand the role they perform in the integrity of the building materials considering the climatic and environmental conditions.