Inland Antarctic terrestrial ecosystems and biodiversity are poorly understood in comparison with Antarctic coastal regions. Microorganisms, as primary colonists, are integral to Antarctic soil ecosystem development, essential for pedogenesis and structuring the soil, and providing the nutrients necessary for the subsequent establishment of macroorganisms. This study analysed the microbial communities present in polygon soils of Coal Nunatak (Alexander Island, at the southern limit of the maritime Antarctic). Soils were analysed across three polygons (centre and margins) and at three depths (0–1, 1–2, 2–5 cm). Cyanobacterial communities were characterised using two complementary molecular biological approaches, temperature gradient gel electrophoresis and clone library analysis. The three polygons exhibited conspicuous differences in community composition, both between different polygons and spatially (horizontally and vertically) within a single polygon. Comparison of our data with that from previous studies using classical culture and morphological identification techniques clearly shows the need for more intensive research on patterns of microbial diversity in terrestrial habitats throughout the Antarctic. The majority of the 17 cyanobacterial genera identified at Coal Nunatak are thought to have ubiquitous distributions, while none are known only from the Antarctic. Three of the genera present are also known to be capable of being lichen photobionts.