Endolithic algae from fossiliferous limestones, crystalline limestones and sandstones collected in desert areas of Israel and California were studied with reflected light and scanning electron microscopes. The rocks which are colonized by endolithic algae are light-coloured and their texture is porous. On the surface, there is a 0.1–3.0 mm thick crust where the airspaces between rock particles are filled by mineral substance. The crust is permeable to liquids and gases but impervious to cellular organisms. Algal species of the genus Gloeocapsa which form monospecific populations appear as a 0.1–2.5 mm thick blue-green zone under the surface crust. They grow in the internal airspace system of the rock, cell colonies adhering to the crystals. Whereas the desert macroclimate is “hostile” to free-living microscopic algae, the endolithic environment is well suited to support algal life. Irradiation is filtered to a proper level and the porous rock covered by the surface crust constitutes a system which retains humidity and ensures suitable temperature. It is suggested that endolithic algae contribute to rock weathering.