All other fungi are clearly distinct from other groups and constitute a natural group of related organisms. They resemble each other in general organization of the somatic thallus and in their modes of reproduction and metabolism, and are likely to be derived from a common ancestor. These fungi are the true-fungi. It is ironic that recent DNA sequencing places true fungi closer to animals than plants.
According to one view, the chytridiomycetes evolved from some non green protozoan ancestors. The chytridiomycetes are predominantly terrestrial as are the ascomycetes and basidiomycetes. Mycologist in general agree that the basidiomycetes evolved from the ascomycetes. This view is based largely on the similarity of the clamp connections of the basidiomycetes with the crozier formation in the ascomycetes. Basidiomycetes and ascomycetes show a considerable amount of similarity during the development of the basidium and basidiospores, and the ascus and ascospores. The basidium, according to one view is an evolutionary modification of the ascus, which in turn evolved from the reproductive to one view is an evolutionary modification of the ascus, which in turn evolved from the reproductive structure of zygomycetes. Ascus and basidium are presumed to be homologous structures. In both, the plasmogamy us not immediately followed by Karyogamy.
As against this essentially monophyletic origin of the true fungi in which evolution took place from a single ancestral stock, some mycologists who believe in algal origin of true fungi have suggested that zygomycetes may have evolved directly from a green algal ancestor similar to modern conjugating Spirogyra. Another possibility is that the ascomycetes have an independent origin from some red algal ancestors. This would imply that the chytridiomycetes and the the zygomycetes did not evolve any further into higher categories of taxa. Those who favor red algal ancestry for the ascomycetes find similarities in the fungal fruiting bodies such as cleistothecia and perithecia and the red algal cystocarp in the non motile spermatia and the trichogyne that occur in many red algae and some true fungi, and in the special thickenings that occur in the cross-walls of red algae and basidiomycetes.