This set of files contain the 16S rDNA, taxonomic assignments from the greengenes database, and the R script for processing the data. Abstract Lava caves around the world often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. We generated and analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soils overlying each cave. Actinobacteria dominated in all samples, with 39% (caves) and 21% (surface soils). Proteobacteria made up 30% of phyla from caves and 36% from surface soil with Gamma- 20% and Alpha- 10% in the caves and Gamma- 18% with Alpha-17% in soil. Other major phyla in caves were Nitrospirae (7%) followed by Minor Phyla (7%), compared to surface soils with Bacteriodetes (8%) and Minor phyla (8%). A very high proportion (53.33%) of the most abundant sequences could not be identified to genus, indicating a high degree of novelty. Surface soil samples had more OTUs and greater diversity indices than cave samples. The same phyla were represented in both soils and cave microbial mats, but the overlap was only 11.2% at the operational taxonomic unit (OTU). Although surface soil microbes immigrate into underlying caves, the environment selects for microbes able to live in the cave habitats, resulting in very different cave microbial communities. In terms of species richness, diversity by mat color differed, but not significantly. Number of entrances per cave, distance from an entrance, cave length, and temperature also contributed to observed differences in diversity. With high levels of novel microbes, caves may represent excellent habitats for the isolation of new bioactive compounds. This study is the first comprehensive comparisons of bacterial communities in lava caves with the overlying soil community.