The microbial community colonizing the animal gut includes all domains of life, including eukaryotic microbes. Historically viewed as pathogens, increasing evidence has revealed that many protists are commensal members of the microbiome with diverse ecological functions. This review synthesizes recent advances in our understanding of the ecology and evolution of these organisms, with a focus on phylogenetic diversity, microbial interactions, and genomic signatures of adaptation. New technologies such as single-cell genomics and transcriptomics, long-read sequencing technologies, and co-culture strategies have made these new findings possible, but much remains to be investigated. Further work is needed to understand how these diverse organisms contribute to the gut environment and evolve to colonize animal hosts.