Marine-derived fungi represent a promising resource for biotechnological and pharmaceutical applications. The Southeast Asian region, known for its rich marine biodiversity, harbors a diverse assemblage of fungal species that could be exploited to produce bioactive secondary metabolites. This chapter highlights the potential of this fungal group for drug discovery, industrial processes, and sustainable bioproducts as exemplified by reports on species identified from Southeast Asia. The immense diversity of marine fungi from various sources collected along the coastlines and coastal waters in selected countries in Southeast Asia is also presented. This highlights the immense potential of the region for bioprospecting of fungal natural products.