The recently inaugurated Belgian Princess Elisabeth Station has been built in the Sør Rondane Mountains (Dronning Maud Land). The construction site is situated close to the Utsteinen Nunatak (71°57′S, 23°20′E), on a granite ridge. Prior to the survey and construction activities, the site had been subject to limited or no direct human impacts. Therefore, a biological inventory has been started for future evaluations of human impacts in the area. This study presents the cyanobacterial diversity of ten samples from the Utsteinen ridge, the Utsteinen Nunatak in the vicinity of the station's site and the more distant Ketelersbreen Dry Valley. All samples were taken before the station was built and were studied by light microscopy and Denaturing Gradient Gel Electrophoresis. Two strains were also isolated. Two different phenol-based extraction methods, with and without detergent-based steps, were tested to improve the quality of molecular detection from these environmental samples. We observed high cyanobacterial diversity (ten morphotypes and 13 operational taxonomic units) in comparison to other Antarctic terrestrial locations and a widespread distribution pattern within the Sør Rondane Mountains area. This might reflect the habitat similarities and/or the easy local dispersal capabilities of microorganisms within the region. The high diversity and proportion of potential endemic (46%) operational taxonomic units, of which 23% were newly described, suggest that this area could have acted as a biological refuge during past glaciations.