Fairy Circles (FCs) are barren circular patches of soil surrounded by grass species, the origin of which is poorly understood. FCs feature in both the gravel plains and dune fields of the Namib Desert. While a substantial number of hypotheses to explain the origin and/or sustainability of fairy circles have been presented, none are completely consistent with either their properties or distribution. In this study, we investigated the hypothesis that dune and gravel plain FC formation is due to microbial phytopathogenesis. Surface soils from five gravel plain and five dune FCs, together with control soil samples, were analysed using high-throughput sequencing of bacterial/archaeal (16S rRNA gene) and fungal (ITS region) phylogenetic markers. Our analyses showed that gravel plain and dune FC microbial communities are phylogenetically distinct and that FC communities differ from adjacent vegetated soils. Furthermore, various soil physicochemical properties, particularly pH, Ca, P, Na, SO4, soil particle size and % carbon, significantly influenced dune and gravel plain FC microbial community compositions but none were found to segregate FC and vegetated soil communities. Nevertheless, 9 bacterial, 1 archaeal and 57 fungal phylotypes were identified as FC-specific, being present only within the gravel plain and dune FCs soils but not in the vegetated soils. Some of these FC-specific phylotypes were assigned to taxa known to harbour phytopathogenic microorganisms. This suggests that these FC-specific microbial taxa may be involved in the formation and/or maintenance of Namib Desert FCs.