Molecular data has been used in fungal systematics since the 1970s, and its rate of incorporation has increased significantly in recent years. In phylogeny molecular data has already been used to clarify major evolutionary lines, and has aided in the delineation of higher taxonomic groups including the kingdom Fungi, and the main phyla within it. Molecular data has been used at all taxonomic levels and has allowed for a greater phylogenetic signal to be represented within systematic groups. At the higher levels this has led to the re-evaluation of some orders and families, and at lower taxonomic levels it has helped in the identification of species, particular populations and possibly individuals. There are however some limitations to the widespread use of molecular data. Some of these relate to the comparability and utility of methods between different fungal groups, some relate to the wide diversity of life cycles adopted by fungi, and others are due to the paucity of comparable definitive evolutionary markers. A significant limitation to the wider application of molecular data is the restricted range of data currently available, and the relation of this to the as yet unquantified numbers of undescribed species. Despite these limitations molecular data has had a very significant effect on our understanding of fungal systematics, and many further systematic aspects are likely to be elucidated in the future.