The advances that have been made on the effect of lichens on rock substrate have been numerous. The first techniques used in order to know the type of biodeterioration produced by lichen thalli, were observations by light microscopy. The microchemical techniques that followed this, such as X-Ray Diffraction and Infrared Spectroscopy, provided knowledge of the mineral composition of the substrate which is in contact with the lichen thalli. This zone is known as interface. More recently, the Scanning Electron-Microscope has allowed observations of the relationship between the hyphae of the lower part of the thallus and the topography of the superficial part of the rock. In the current work, new applications of Scanning Electron Microscopy are presented. The backscattered electron image permits observation of the penetration of living thalli elements in the rock. With this technique, it is possible to follow the fissures underneath the lichen thalli and see at a cellular level the biological elements. This technique is an important step in understanding the biodeterioration produced by lichens. It allows clarification of such aspects as the ability of embedded minerals detached from the rock among the hyphae and also the possibility of investigating organic and inorganic compounds mixed with hyphae and algae. This technique, moreover, is promising for use in future investigations of biodeterioration where the cellular morphology of the different organisms are interesting, taking into account treatments with biocides.