Soil-dominated ecosystems, with little or no plant cover (i.e. deserts, polar regions, high-elevation areas and zones of glacial retreat), are often described as ‘barren’, despite their potential to host photoautotrophic microbial communities. In high-elevation, subnival zone soil (i.e. elevations higher than the zone of continuous vegetation), the structure and function of these photoautotrophic microbial communities remains essentially unknown. We measured soil CO2 flux at three sites (above 3600 m) and used molecular techniques to determine the composition and distribution of soil photoautotrophs in the Colorado Front Range. Soil CO2 flux data from 2002 and 2007 indicate that light-driven CO2 uptake occurred on most dates. A diverse community of Cyanobacteria, Chloroflexi and eukaryotic algae was present in the top 2 cm of the soil, whereas these clades were nearly absent in deeper soils (2–4 cm). Cyanobacterial communities were composed of lineages most closely related to Microcoleus vaginatus and Phormidium murrayi, eukaryotic photoautotrophs were dominated by green algae, and three novel clades of Chloroflexi were also abundant in the surface soil. During the light hours of the 2007 snow-free measurement period, CO2 uptake was conservatively estimated to be 23.7 g C m−2 season−1. Our study reveals that photoautotrophic microbial communities play an important role in the biogeochemical cycling of subnival zone soil.