The deterioration of stone monuments is a process of deterioration of rocks in nature. In other words, both inanimate factors like wind, rain and others, and animate factors like animals, plants and microorganisms contribute in the formation of soil from rocks. Since the role of organisms in soil formation is especially great, ways of controlling the deteriorating effects of organisms are a topic of great importance. When rocks in nature gradually form soil upon the earth, the first organism to appear is believed to be lichens. After this, organic and inorganic substances on the surface of rocks are affected by various types of microorganisms, and their metabolic products also influence the formation of soil. In addition, roots of trees penetrate into the rocks and destroy them. Such cases are observed in various regions. Soil formation from rocks in nature is directly related to the deterioration of stone monuments, and because the deterioration of stone constructions are brought about by the same phenomenon, it is necessary to have a clear grasp of the mechanism of this deterioration. The author first surveyed the ages of stone monuments in Japan, their materials, locations and conditions of their deterioration. The mechanism of deterioration caused by trees, by algae, by lichens, and by soil microorganisms are explained respectively. Microbiological analyses of deteriorated tuff and sandstone and granite in Japan were conducted. Microbiological analysis was carried out on the samples of flaky products found in the process of conservation and restoration of the Monument of Borobudur, and the result is shown. The methods for removing lichens in Indonesia are introduced.