Anaerobic fungi are the primary colonizers of biomass within the digestive tract of large herbivores, where they have evolved unique abilities to break down lignin-rich cellulosic biomass through invasive, filamentous growth and the secretion of powerful lignocellulolytic enzymes. Despite these attractive abilities, considerably less genomic and metabolic data exists for gut fungi compared to well-studied anaerobic bacteria and aerobic fungi that hydrolyze cellulose. We have addressed these knowledge gaps by isolating and characterizing a collection of fungi from large herbivores using a combination of ‘omics’ tools. Hundreds of novel carbohydrate active enzymes (CAZymes) and components of fungal cellulosomes (enzyme complexes) were identified from several strains of anaerobic fungi, which were discovered through a combination of homology modeling and catabolite repression. Many of these CAZymes share high homology with those found in anaerobic bacteria, and likely arose through horizontal gene transfer. Additionally, high-resolution genomic sequences have revealed a rich set of biosynthetic genes across the fungi that likely regulate diverse processes from fungal development and maturation to microbial defense in the rumen microbiome. A wealth of diverse membrane transporters (SWEET, MFS, etc.) were also identified across anaerobic fungal genomes, which were verified to enhance sugar transport activity in the yeast S. cerevisiae. Overall, our work has unmasked a rich repertoire of novel biomass-degrading enzymes, transporters, biosynthetic gene clusters, and a wealth of horizontally transferred genes within the rumen microbiome that can be used for synthetic biology and the engineering of model microorganisms.