Fungi in the human gut microbiota participate in the maintenance of health and regulation of physiological processes. This review examines the complex role of gut fungi, highlighting challenges such as diverse fungal populations, cultivation difficulties, and knowledge gaps in their functional roles. Recent advancements in metagenomics and metabolomics have enabled innovative investigations into fungal communities, revealing their influence on host metabolism and immune responses. Future research should address the existing knowledge gaps and explore the therapeutic applications of gut fungi. Interdisciplinary collaborations and new methodologies are proposed to enhance the current understanding of fungi-host interactions, ultimately improving health outcomes and guide the development of novel treatment strategies. This review emphasizes the need to integrate fungal research into microbiome studies to provide a comprehensive understanding of gut health.