© Jens H. Petersen, Department of Systematic Botany, Biological Institute, University of Aarhus, Denmark

This outline of the Zygomycota is largely derived from Ainsworth, G.C., F.K. Sparrow & A.S. Sussman (eds.) : The Fungi, 1973. It is thus not a very modern system, but as far as I know, nobody has since published a coherent system to the Zygomycota.
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Link to a tree : T
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Genera containing lichenized species are coloured yellow
Genera containing mycorrhizal species are coloured green
Genera containing biotroph parasites species are coloured red
| Zygomycetes | ||||
| Mucorales | ||||
| Endogonales | ||||
| Glomales | ||||
| Entomophthorales | ||||
| Zoopagales | ||||
| Trichomycetes | ||||
| Harpellales | ||||
| Asellariales | ||||
| Eccrinales | ||||
| Amoebidiales | ||||
| Zygomycetes | ||||
| Mucorales | ||||
| Choanephoraceae | ||||
| Choanephora, Gilbertella | ||||
| Cunninghamellaceae | ||||
| Cunninghamella | ||||
| Dimargaritaceae | ||||
| Dimargaris | ||||
| Heliococephalidaceae | ||||
| Rhopalomyces, Helicocephalum | ||||
| Kickxellaceae | ||||
| Spirodactylon, Spiromyces, Kickxella, Martensiomyces, Linderina, Dipsacomyces, Martensella, Coemansia | ||||
| Mortierellaceae | ||||
| Aquamortierella, Dissophora, Haplosporangium, Mortierella | ||||
| Mucoraceae | ||||
| Absidia, Actinomucor, Mucor, Rhizopus, Spinellus | ||||
| Pilobolaceae | ||||
| Pilaria, Pilobolus | ||||
| Piptocephalidaceae | ||||
| Piptocephalis, Syncephalis | ||||
| Radiomycetaceae | ||||
| Hesseltinella, Radiomyces | ||||
| Saksenaeaceae | ||||
| Echinosporangium, Saksenaea | ||||
| Syncephalastraceae | ||||
| Syncephalastrum | ||||
| Thamnidiaceae | ||||
| Chartocladium, Chartostylum, Cokeromyces, Dicranophora, Helicostylum, Thamnidium, Thamnostylum | ||||
| Endogonales | ||||
| Endogonaceae | ||||
| Endogone, Sclerocgone | ||||
| Glomales | ||||
| Glomaceae | ||||
| Glomus, Sclerocystis | ||||
| Acaulosporaceae | ||||
| Acaulospora, Entrophospora | ||||
| Gigasporaceae | ||||
| Gigaspora, Scutellospora | ||||
| Entomophthorales | ||||
| Entomophthoraceae | ||||
| Ancylistes, Basidiobolus, Completoria, Conidiobolus, Entomophthora, Massospora | ||||
| Zoopagales | ||||
| Zoopagaceae | ||||
| Acaulopage, Cystopage, Stylopage, Zoopage | ||||
| Cochlonemaceae | ||||
| Amoebophilus, Aplectosoma, Bdellospora, Endocochlus, Euryancale | ||||
| ? Trichomycetes | ||||
| Harpellales | ||||
| Harpellaceae | ||||
| Carouxella, Harpella, Stachylina | ||||
| Genistellaceae | ||||
| Genistella, Genistellospora, Glotxia, Graminella, Orpella, Penella, Pteromakton, Simuliomyces, Smittium, Spartiella, Stipeila, Trichozygospora | ||||
| Asellariales | ||||
| Asellariaceae | ||||
| Asellaria, Orchesellaria, Trichoceridium | ||||
| Eccrinales | ||||
| Eccrinaceae | ||||
| Alacrinella, Arundinula, Astreptonema, Eccrinidus, Eccrinoides, Enterobryus, Enteromyces, Ramacrinella, Taeniella, Taeniellopsis | ||||
| Palavasciaceae | ||||
| Palavascia | ||||
| Parataeniellaceae | ||||
| Lajassiella, Parataeniella | ||||
| Amoebidiales | ||||
| Amoebidiaceae | ||||
| Amoebidium, Paramoebidium | ||||