Ecosystems with little or no plant cover are often described as barren, however these systems can host diverse microbial communities. Yet, the biological functioning of these soils in high-altitude mountain ecosystems is poorly understood. We measured soil CO₂ fluxes and used molecular techniques to determine the composition of the bacterial and eukaryotic community at “barren” high-elevation sites in Colorado. Seasonal measurements of soil CO₂ flux were made throughout the snow-free periods of 2002 and 2007, and these data showed that light-driven CO₂ uptake occurred on most dates. In addition, we found a diverse community of Cyanobacteria, Chloroflexi and eukaryotic algae within the top two centimeters of the soil, whereas these clades were nearly absent in deeper soils (2-4 cm). The Cyanobacterial communities of the surface soil were composed of lineages most closely related to Microcoleus vaginatus and Phormidium murrrayi, and the major clades were frequently site specific. Eukaryotic sequences indicate that the soils are dominated by green algae from the Chlorophyceae and Trebouxiophyceae. Three novel clades of Chloroflexi were also found to predominate within the top 2 cm of the soil. One of these clades is most closely related to known photoautotrophic Chloroflexi. During the light hours of the snow-free period in 2007, CO₂ uptake was conservatively estimated to be 24 g C m^-2 yr^-1, far greater than the estimated 0.5 g C m^-2 yr^-1 deposited via eolian deposition. These data counter current theory by suggesting that eolian deposition is not the dominant source of carbon within subnival zone soil. Taken together, these data suggest that photoautotrophic communities play an important role in the biogeochemical cycling of subnival zone soil and that the soil may harbor both known and novel photoautotrophic microorganisms.