Fungi are the major microbes to exploit fiber degrading enzymes. Anaerobic fungi possess hydrogenosomes and cellulosomes to improve their energy supply in anaerobic environment, and their thick cell wall or spore-like structure help them adapt adverse environment. Animal host phylogeny and diet exert the most significant role in shaping anaerobic fungal diversity and community structure. Molecular marker technology based on ribosomal 18S/28S rRNA genes and internal spacer region (ITS) provides a more precise means for the research of anaerobic fungi quantity and diversity, and the 28S rDNA D1/D2 is the preferred region for anaerobic fungal next generation sequencing. Due to limited databases for fungus and methods for obtaining enough fungal DNA/RNA from digestive tract contents for metagenomic/metatranscriptomic analyses, little work is available on fungal physiology and function of gastrointestinal tract using advanced omics techniques. However, application of these techniques will be key to deepen our understanding of the ecological role of fungi in gastrointestinal tract.