Studies on the molecular diversity of the micro-eukaryotic community have shown that fungi occupy a central position in a large number of marine habitats. Environmental surveys using molecular tools have shown the presence of fungi from a large number of marine habitats such as deep-sea habitats, pelagic waters, coastal regions, hydrothermal vent ecosystem, anoxic habitats, and ice-cold regions. This is of interest to a variety of research disciplines like ecology, evolution, biogeochemistry, and biotechnology. In this review, we have summarized how molecular tools have helped to broaden our understanding of the fungal diversity in various marine habitats. Majority of the environmental phylotypes could be grouped as novel clades within Ascomycota, Basidiomycota, and Chytridiomycota or as basal fungal lineages. Deep-branching novel environmental clusters could be grouped within Ascomycota as the Pezizomycotina clone group, deep-sea fungal group-I, and soil clone group-I, within Basidiomycota as the hydrothermal and/or anaerobic fungal group, and within Chytridiomycota as Cryptomycota or the Rozella clade. However, a basal true marine environmental cluster is still to be identified as most of the clusters include representatives from terrestrial regions. The challenge for future research is to explore the true marine fungi using molecular techniques.