We characterized the microbes that are attached to deep-water moss in Crater Lake, Oregon. Moss leaves are densely colonized with a microbial community that differs from that found in the water column. Most notably, the cyanobacterial epiphytes on Crater Lake's moss are absent from the water column. Algal and cyanobacterial moss epiphytes were surveyed and identified using microscopy and gene sequencing. We found that diatoms and filamentous algae took up the greatest surface area on moss, with cyanobacterial epiphytes present in fewer numbers. Heterotrophic bacteria were more abundant on moss leaves than eukaryotes but occupied far less surface area. Eukaryotic large subunit rRNA gene sequences obtained from moss DNA extracts verified the presence of several different genera of algae associated with moss. In addition, sequence analysis revealed the presence of symbiotic fungi and protozoa. To identify prokaryotic nitrogen fixers on moss, nitrogenase and nitrogenase-like gene sequences were obtained from moss epiphytes. All of the nitrogenase genes associated with moss epiphytes were cyanobacterial sequences. In contrast, no nitrogenase sequences were detected in the water column. In addition, we cultured and identified four different genera of cyanobacteria from Crater Lake moss leaves. Given that Crater Lake has virtually undetectable levels of nitrate in the zone where moss grows most abundantly, the nitrogen fixing ability of cyanobacterial epiphytes is likely to provide a growth advantage to cyanobacteria and to nearby organisms.