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Most studies investigating the effects of climatological factors on microbial community composition and diversity focus on comparisons of geographically distinct environments (e.g., cold vs hot deserts) or across various temporal scales. Mountain regions provide unique environments to explore relationships between various environmental factors and soil microorganisms given their range of microclimatic conditions and vegetation types. This study investigated micro‐topographically (i.e., north‐/south‐facing slope aspects and flat plateau between them) controlled microbial diversity and community structures across a Lesotho mountain summit. Amplicon sequence analysis revealed that the north‐ and south‐facing slopes were dominated by more Proteobacteria and Bacteroidetes, while the plateau was dominated by more Acidobacteria. Fungi from the phylum Chytridiomycota more strongly dominated the plateau and the north‐facing slope than the south‐facing slope. Slope aspect, through its direct influence on air and soil micro‐climatology and plant diversity, significantly affects bacterial and fungal community structures at this location. These results provide original insight into soil microbial diversity in the Lesotho highlands and offer an opportunity to project the likely response of soil microorganisms to future climate warming in highly variable mountain environments such as the Lesotho highlands. [ABSTRACT FROM AUTHOR]