Evidence of climate-driven environmental change is increasing in Antarctica, and with it comes concern that this will propagate to impacts on biological communities. Recognition and prediction of change needs to incorporate the extent and timescales over which communities vary under extant conditions. However, few observations of Antarctic microbial communities, which dominate inland habitats, allow this. We therefore carried out the first molecular comparison of Cyanobacteria in historic herbarium microbial mats from freshwater ecosystems on Ross Island and the McMurdo Ice Shelf, collected by Captain R.F. Scott's ‘Discovery’ Expedition (1902–1903), with modern samples from those areas. Using 16S rRNA gene surveys, we found that modern and historic cyanobacteria assemblages showed some variation in community structure but were dominated by the same genotypes. Modern communities had a higher richness, including genotypes not found in historic samples, but they had the highest similarity to other cyanobacteria sequences from Antarctica. The results imply slow cyanobacterial 16S rRNA gene genotype turnover and considerable community stability within Antarctic microbial mats. We suggest that this relates to Antarctic freshwater 'organisms requiring a capacity to withstand diverse stresses, and that this could also provide a degree of resistance and resilience to future climatic-driven environmental change in Antarctica.