eThe hindguts of lower termites and Cryptocercus cockroaches are home to a distinct community of archaea, bacteria, and protists (primarily parabasalids and some oxymonads). Within a host species, the composition of these hindgut communities appears relatively stable, but the evolutionary and ecological factors structuring community composition and stability are poorly understood, as are differential impacts of these factors on protists, bacteria, and archaea. We analyzed the microbial composition of parabasalids and bacteria in the hindguts of Cryptocercus punctulatus and 23 species spanning 4 families of lower termites by pyrosequencing variable regions of the small-subunit rRNA gene. Especially for the parabasalids, these data revealed undiscovered taxa and provided a phylogenetic basis for a more accurate understanding of diversity, diversification, and community composition. The composition of the parabasalid communities was found to be strongly structured by the phylogeny of their hosts, indicating the importance of historical effects, although exceptions were also identified. Particularly, spirotrichonymphids and trichonymphids likely were transferred between host lineages. In contrast, host phylogeny was not sufficient to explain the majority of bacterial community composition, but the compositions of the Bacteroidetes, Elusimicrobia, Tenericutes, Spirochaetes, and Synergistes were structured by host phylogeny perhaps due to their symbiotic associations with protists. All together, historical effects probably resulting from vertical inheritance have had a prominent role in structuring the hindgut communities, especially of the parabasalids, but dispersal and environmental acquisition have played a larger role in community composition than previously expected.C ryptocercus cockroaches and their sister lineage, the lower termites (1), are both dependent on diverse communities of microorganisms in their hindguts to gain nutrition from lignocellulose (reviewed in references 2 and 3). These are fascinating and complex communities dominated by parabasalid (Parabasalia) and oxymonad (Preaxostyla) protists (4) as well as numerous bacterial lineages, including Actinobacteria, Bacteroidetes, Elusimicrobia, Firmicutes, Proteobacteria, Spirochaetes,. Moreover, a large proportion of the bacteria form obligate symbiotic interactions with the protists (see, for example, references 8-14), so the community contains multiple levels of symbiosis. Because of the diversity of symbionts, the hindguts of Cryptocercus cockroaches and lower termites can be used as model systems to study the ecology and interactions between protists and bacteria. Here, we investigate the ecological and evolutionary differences between protists and bacteria in structuring community composition. These differences are critical to understanding the diversification and adaptation of microbes, the stability and resilience of community structure, and the maintenance of ecosystem functions, particularly in regard to understanding lignocellulose digestion...