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To investigate the composition of the microbial community in biodeterioration of two frescoes in St Damian's Monastery in Assisi.A total of 1292 colonies were isolated from the most deteriorated parts, analysed by microbiological, biomolecular and ultrastructural techniques, and taxonomically classified. Molecular biotyping of Staphylococcus cohnii colonies, one of the most prevalent bacterial species, showed a very restricted genome diversity while Bacillus licheniformis were very homogeneous by RFLP, tDNA-PCR and random-amplified polymorphic DNA. Electron microscopy confirmed heterogeneity of the bacterial population in the different sampling areas.Several of the identified species are widespread in the soil or saprophytes of human skin. Although unable to demonstrate that they are involved in biodeterioration, they may represent trophic elements contributing to fungi-related chromatic alterations when adequate environmental conditions occur. Deterioration may in part be prevented or controlled by adequate air filtering or conditioning of the room.