Studies of human–associated microbial communities are increasingly integrated into biological anthropology, allowing us to explore the role of microorganisms in aspects of human evolution, health, and disease. Despite technological advances in the genomic characterization of microbial ecosystems in both modern populations and in the past, specific challenges remain in documenting the presence of taxa, functional potential, and interaction of members of these dynamic ecosystems. In this dissertation, three studies designed to address some of the challenges of metabarcoding and metagenomic studies of the modern human gut and ancient oral microbiome are presented. In chapter two, the eukaryotic component of the modern human gut is assessed with a metabarcoding approach using the internal transcribed spacer region. In chapter three, rare bacterial taxa are characterized using a joined serial filtration and metabarcoding approach. Finally, in chapter four, the preservation of ancient DNA in archaeological dental calculus is discussed with particular attention to both the benefits of this substrate as a reliable source of ancient DNA as well as the potential challenges associated with DNA preservation in archaeological materials.