Tropical climate create ideal conditions for the development of microbial communities associated with biodegradation of historic buildings made with stony materials. This is the case of Fort San Carlos, a historic colonial building representative of military tendencies during the XVII century in San Francisco de Campeche City. In this study the Polymerase Chain Reaction (PCR), was used to identify microorganisms related with the biodegradation of its masonry structure. Specific primers for amplification of 16S and 18S ribosomal RNA genes were used for organisms identification by PCR. Amplification products were sequenced and after that compared with GENBANK nucleotide database using-BLASTn. Results indicated that microbial communities associated to biodegradation of the Fort San Carlos are bacteria from the Phyla Cyanobacteria, Proteobacteria and Actinobacteria.