Caves and other extreme environments harbor unique microbial communities, particularly fungi, which exhibit remarkable adaptations to conditions such as nutrient limitation, constant darkness, and high humidity. Cave fungi predominantly from the phyla Ascomycota, Basidiomycota, and Mucoromycota utilize substrates such as bat guano, decomposing organic matter, and mineral surfaces. They play important roles in cave ecosystems by recycling nutrients, maintaining ecological balance, and supporting food webs. These fungi perform various functions, from decomposition to pathogenicity, with some species causing diseases like white-nose syndrome in bats and histoplasmosis in humans. The extreme conditions within caves promote the production of secondary metabolites with antimicrobial, anticancer, and enzymatic properties, making cave fungi as possible sources of novel bioactive compounds. Fungal diversity is affected by both abiotic factors, such as temperature, humidity, and substrate type, and biotic interactions involving bats, insects, and other microorganisms. To investigate these communities, researchers utilize a combination of culture-dependent and omics-based approaches. Beyond cave ecosystems, fungi inhabiting other extreme environments, such as salterns, acidic mangrove sediments, glaciers, and deep-sea ecosystems, exhibit similar stress-tolerance mechanisms, including melanin production, siderophore synthesis, and thermotolerance, which enable survival under extreme environmental conditions. Despite their ecological importance and biotechnological potential, studying cave fungi is faced with notable challenges, including limited accessibility, low culturability, contamination risks, and ethical concerns regarding the conservation of fragile cave ecosystems. Nonetheless, cave fungi present valuable insights into microbial evolution, environmental stress adaptation, and ecosystem functioning, with potential for applications in drug discovery and biotechnology. In Southeast Asia, particularly the Philippines, fungal diversity in extreme environments like caves remains largely unexplored, emphasizing the need for interdisciplinary, conservation-focused research initiatives. This chapter explores the diversity, ecological functions, and biotechnological potential of fungi in these habitats, emphasizing their significance in light of a changing climate.