With the advancement of molecular techniques in the last two decades, cultures of marine fungi have been sequenced, and several new lineages of marine fungi have been revealed, suggesting multiple evolution of fungi into the marine environment. High-throughput sequencing has also allowed discovery of unculturable marine fungi, such as the Cryptomycota. Traditionally, marine fungi are known to belong mostly to the Ascomycota and asexual morphs with few basidiomycetes and chytrids. In this chapter, we will introduce the phylogenetic diversity of these groups with the emphasis on the ascomycetous classes Dothideomycetes and Sordariomycetes, where most marine ascomycetes are referred to. We will also summarize the current knowledge on the marine taxa at the basal lineages of fungi including the phyla Aphelida, Cryptomycota, and Microsporidia, currently classified in the superphylum Opisthosporidia.