Lichens are commonly described as a mutualistic symbiosis between fungi and "algae" (Chlorophyta or Cyanobacteria); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated by Alphaproteobacteria. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associated Rhizobiales lineage (LAR1; putative N 2 fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N 2 fixers (e.g., Azospirillum, Bradyrhizobium, and Frankia) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses.Marine sponges (31), the termite hindgut (34), mycorrhizal fungi (2, 13), and fungal endophytes (18) represent symbiotic niches where unique interactions between eukaryotes and rich, diverse bacterial populations occur. Lichens, a relationship between fungi (mycobionts, on which the species names and classifications are based) and green algae and/or cyanobacteria (photobionts), are another symbiotic niche that has received recent attention (15). Lichen thalli host diverse populations of organisms, such as lichenicolous (growing on the thallus) (21) and endolichenic (growing within the thallus) fungal species (1). While nonphotosynthetic bacteria have long been suspected to be associated with lichens (32; but also see reference 8), modern culture-independent studies are just beginning to reveal the diversity in bacteria inhabiting lichens, suggesting that lichens host diverse assemblages from several bacterial phyla (7,8,14,16,17,23).The few studies that have characterized the bacterial communities of lichens by using molecular fingerprinting techniques are limited in their phylogenetic resolution and have yielded conflicting results. Grube et al. (16) found that the community composition for certain lichen-associated bacterial groups (e.g., Alphaproteobacteria) exhibited species-specific patterns, and they advanced the idea that bacteria may be integral to the lichen symbiosis. Cardinale et al. (8), however, concluded that the structure of bacterial communities in lichens was not correlated with the host species and...