Fungi are separated into phyla on the basis of their reproductive structures. Because some fungi have never been observed to reproduce sexually, they have no place in the classification. Until their sexual reproduction is identified they are placed in Fungi Imperfecti (Deuteromycetes). DNA sequencing is giving the mycologists answers. Most of the taxa so far sequenced and classified are ascomycetes, with only a few basidiomycetes and fewer still zygomycetes. Another problem group is the Chytridiomycota (chytrids), which arguably may belong with the Protoctists, not the fungi.
No clearcut ancestral lineage for the fungi has been established, but on the basis of molecular DNA sequencing and morphological evidence it seems likely that the fungal life style arose many times from different protoctists. The fungi and animals are on the same originating branch. Within the modern fungi, the chytrids are the oldest of the group with the ascomycetes and basidiomyctes closely related and on a different, more recent line from the zygomycetes.
Evidence of fungi growing within the cells of 400‐million‐year‐old Silurian‐Age vascular plants suggests an early origin for the fungi. The first fungi developing from very early eukaryotes undoubtedly were unicellular; coenocytic filamentous forms were a later development.
An interesting proposal postulates that a symbiosis between early fungi and early plants permitted the plants to establish themselves on land before they had evolved roots with which to absorb vital water and minerals from the soil. The fungi could do this for them and already were associated with some plants, hence the start of the mycorrhizal association.