To establish a routine procedure for surveying lichen diversity in biological soil crusts across different biomes in Southern Africa (Namibia and the western part of South Africa), the use and analysis of digital plot images proved to be most effective. Soil lichen taxa were classified into ‘morphological groups’ (MGs) which could be easily recognized by imaging systems. MGs were defined by the presence and variance of two macro-morphological traits (growth form and colour of the thallus surface) and the type of the primary lichen photobiont. A classification is presented. The distribution of the various lichen MGs and their cover were assessed by analyzing soil surface digital images. Richness of lichen species and MG cover were compared on the basis of these image data. Results show that lichen richness at hectare plot and at 1 km² level strongly correlates with lichen morphogroup richness, while the total lichen cover on the same plot has a weaker relationship with species and MG richness. Lichen richness at the hectare plot level is strongly associated with morphogroup richness, and is correlated with increasing air humidity and winter rainfall but negatively linked with higher temperatures. The use of morphogroups corresponds to the temporal and spatial cover of soil lichen biodiversity in Southern Africa, with no significant loss of relevant information.