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