East Africa is one of the most important paleoanthropological localities on Earth. Laetoli and Olduvai Gorge (Tanzania) are among the world’s premier areas for Australopithecus afarensis, Paranthropus boisei, and Homo habilis remains. Laetoli is also unique in its preservation of footprint trails within Tuff 7 left by Australopithecus afarensis. Tuff 7 has been studied to characterize microorganisms living inside these tuffs and to estimate their potential involvement in destructive processes; 35 species of microfungi, as well as sterile white and dark mycelia were identified by cultural method. The results of the metagenomic analysis show that anamorphic ascomycetes are the predominant group in all samples. They occur as hyphae and mycelia inside the tuffs, and are concentrated in pores, microcracks and cavities. The number of micromycetes is moderate (up to 7000 CFU per gram of substrate). Typical cultivated microfungi are from genera Aspergillus and Fusarium. They are known as active destructors of natural and artificial substrates and can colonize building materials. Molecular genetic methods revealed a large group of different bacteria (23 phyla) within the tuff. The microbiota consists mostly of Actinobacteria, Proteobacteria, Bacteroidetes and Cyanobacteria. Their relative distribution shows the preferential occurrence of Bacteroidetes in the upper part of stratigraphic sections (soil), and concentration of Actinobacteria and Proteobacteria within the tuffs. Exposure of the Footprint tuff could lead to the development of photosynthetic microorganisms (Cyanobacteria). We conclude that microbiological activity within the study area appears to be moderate and the Footprint Tuff does not presently require any treatment with biocides. However, the presence of black biofilms on the surface of the Footprint conservation mound concrete shows that biodestruction does occur.