Symbionts—consisting of parasites, commensals, and mutualists that live in or on another organism—represent a large fraction of the total life on Earth. The discipline of ecology has, in despite this reality, tended to focus on macroscopic free-living systems, and the ecological processes that govern symbiont communities remain poorly elucidated in comparison. Uncovering these processes may, however, be important to a range of theoretical and applied biological issues, particularly as advances in next-generation sequencing technologies continue to reveal complex host-associated communities with important roles in health and disease. While research on these host-associated communities has largely focused on prokaryotic microbiomes, conserved functional roles across microbial and macroscopic eukaryotes may make them excellent candidates for evaluating the applicability of general ecological theories to symbiont communities. As ubiquitous non-human primates known to harbor diverse eukaryotic communities with proposed relevance to emerging zoonotic disease risk, long-tailed macaques (Macaca fascicularis) represent excellent hosts for the study of such symbiont. In this dissertation, I test the applicability of general ecological principles to eukaryotic symbionts, with a focus on symbionts of long-tailed macaques living in Singapore and Bali, Indonesia. I use a range of techniques that include classical microscopy-based parasite diagnostics, 18S Small Subunit Ribosomal RNA Gene metabarcoding, and Bayesian phylogenetic inference. I find that long-tailed macaques harbor diverse communities of eukaryotic symbionts with taxonomic richness comparable and functional diversity that is comparable to many free-living systems. I also find evidence for important interactions between constituents of these communities that include internal bottom-up resource-mediated and top-down predation mediated regulation by constituents of these communities, and a role for coinfecting helminthes in modulating host immune pressures on microparasites.I also find evidence for host specific niche space and propagule pressure as drivers of host switching in a ubiquitous group of parasites, the Blastocystis species-complex. Finally, I demonstrate the utility of the ecological approaches that I develop in this dissertation, by applying them to better understand structuring of host usage within Plasmodium knowlesi, a zoonotic malarial agent. Taken together, my findings suggest that free-living and symbiont eukaryotes are governed by similar ecological processes.