The phototrophic microbial community inhabiting exposed dolomite in the alpine Piora Valley (Switzerland) forms a distinct endolithic bilayer that features adjacent red dolomite (exterior) and green dolomite (interior) layers that are c. 0.5-1 mm below the rock surface. Characterization of the community, with an emphasis on cyanobacteria, was conducted with culture-dependent and -independent approaches. Direct microscopy of green dolomite revealed four distinct morphotypes consistent with Chlorophyta genera Chlorella and Stichococcus and the Cyanobacterial genera Nostoc and Calothrix, whereas only Stichococcus and Nostoc were observed in the red dolomite. Enrichment in BG-11 media resulted in the growth of Chlorella and Stichococcus. Denaturing gradient gel electrophoresis (DGGE) analysis of DNA extracted from the enrichment revealed two dominant phylotypes with sequence similarity to Chlorella osrokiniana chloroplast and the cyanobacteria genus Leptolyngbya. 16S rRNA gene-based DGGE analysis of DNA extracted directly from both layers indicated that although both layers harboured phylotypes most similar to the Cyanobacterial genera Nostoc, Chroococcidiopsis, and Microcoleus, and the Chlorophyte Stichococcus bacillaris, the two layers also harboured unique genera such as Scytonema, and Symploca (red, external layer of dolomite) and Chlorella (green, internal layer of dolomite). The unique community structure of each layer suggests a selection process directed by the pressures of the endolithic environment. We conclude that the overall composition of the phototrophic community closely resembles that of endolithic communities located in extreme habitats, suggesting that a cosmopolitan community inhabits this defined niche.