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The order Cantharellales is a lineage of approximately 1,000 fungal species that is sister to the rest of the mushroom-forming fungi (Agaricomycetes). Cantharellales species display a diverse array of morphologies and nutritional modes, from corticioid (crust-like) saprobes that decay dead wood, to biotrophic species that exist as parasites of plants, as well as mycorrhizal mushrooms that form mutualisms with common forest trees. However, the evolutionary relationships among these lineages are poorly known. Within the Cantharellales, I revised the taxonomy of the genus Hydnum (hedgehog mushrooms) in eastern North America by integrating morphological, ecological, and molecular phylogenetic data from modern and historical type collections. I found that sixteen Hydnum species occur in eastern North America alone, in contrast to the five species previously recognized, and all but one species is endemic to the region. I also conducted a systematic and floristic treatment of Cantharellus species (chanterelle mushrooms) from the southern Appalachian Mountains and found that while fruitbody macromorphology is highly variable within and across species, many Cantharellus species are identifiable by a combination of microscopic and ecological characteristics. I described one new species, C. vicinus, from east Tennessee and elevated another taxon to the species level. Furthermore, my results include the first report of the iconic European chanterelle C. cibarius from North America and suggest it may be conspecific with two previously described North American taxa. To construct the first densely sampled multi-locus phylogeny of the Cantharellales, I developed a long-read, high-throughput sequencing method using the PacBio sequencing platform. This method produced clean sequences and allelic variants for multiple loci from hundreds of fresh and dried fungal specimens, cultures, and archival DNA extracts. Using this data, I measured intraspecific haplotype diversity to aid in species delimitation across the Cantharellales and found high levels of within-individual sequence divergence (up to 8.8%), particularly in corticioid Cantharellales with binucleate and multinucleate hyphae. I then combined PacBio and Sanger sequence data to generate the Cantharellales phylogeny, which supports four families in the order. Overall, rpb2 is the most suitable locus for species recognition within Cantharellales.