A fundamental issue in ecology is whether communities are random assemblages or, alternatively, whether there are rules that determine which combinations of taxa can co-occur. For microbial systems, in particular, the question of whether taxonomic groups exhibit differences in community organization remains unresolved but is critical for our understanding of community structure and function. Here, we used presence-absence matrices derived from bar-coded pyrosequencing data to evaluate the assembly patterns of eight bacterial divisions distributed along two Yellowstone National Park hot spring outflow channels. Four divisions (Cyanobacteria, Chloroflexi, Acidobacteria, and Cytophaga-Flavobacterium-Bacteroides) exhibited less co-occurrence than expected by chance, with phototrophic taxa showing the strongest evidence for nonrandom community structure. We propose that both differences in environmental tolerance and competitive interactions within divisions contribute to these nonrandom assembly patterns. The higher degree of nonrandom structure observed for phototrophic taxa compared with the other divisions may be due in part to greater overlap in resource usage, as has been previously proposed for plant communities.