This is a collection of paraphyletic taxa that lie at the base of the fungal tree. There are about three morphological types: the microsporidians (Microsporidiomycota), the flagellated fungi (Chytridiomycota, Neocallimastigomycota, and Basicladiomycota), and the conjugating fungi (Euzygomycota, Parazygomycota, and Glomeromycota).

THE MICROSPORIDIANS

PHYLUM MICROSPORIDIOMYCOTA

• CLASS METCHNIKOVELLOMYCETES
  • ORDER METCHNICOVELLALES.
    • Metchnikovella, Chytridiopsis, Hessea.

• CLASS MICROSPOROMYCETES
  • ORDER GLUGEALES (PLEISTOPHOPIDIDA)
    • Glugea, Perezia, Pleistophora, Telomyxa, Telohania, Amblyospora, Culicospora.
  • ORDER NOSEMALES
    • Nosema, Octosporea, Caudosporea, Mrazekia.

THE FLAGELLATED FUNGI

PHYLUM CHYTRIDIOMYCOTA

• CLASS CHYTRIDIOMYCETES
  • ORDER CHYTRIDIALES:
    • Chytria, Cylindrochytrium, Chytridiomyces, Polyphagus, Synchytrium, .
  • ORDER RHIZOPHIDIALES:
    • Rhizophidium, Kappamyces, Terramyces, Boothiomyces, Batrachochytrium
  • ORDER SPIZELLOMYCETALES:
    • Spizellomyces, Powellomyces, Kochiomyces.

• CLASS MONOBLEPHARIDIOMYCETES
  • ORDER MONOBLEPHARALES:
    • Monoblepharis, Harpochytridium, Oedogoniomyces, Monoblepharella, Gonapodya.

• INCERTAE SEDIS
  • Caulochytridium, Olpidium, Rozella, Rhizophlyctis

PHYLUM NEOCALLIMASTIGOMYCOTA

• CLASS NEOCALLIMASTIGOMYCETES
  • ORDER NEOCALLIMASTIGALES
    • Neocallimastix, Caecomastix, Orpinomyces, Cyllamyces, Piromyces, Anaeromyces.

PHYLUM BLASTOCLADIOMYCOTA

• CLASS BLASTOCLADIOMYCETES (=ALLOMYCETES)
  • ORDER BLASTOCLADIALES (=ALLOMYCALES)
    • Allomyces, Blastocladiella, Blastocladia, Blastocladiopsis, Catenaria, Coelomyces, Microallomyces.

THE CONJUGATING FUNGI

PHYLUM PARAZYGOMYCOTA

• CLASS ENTOMOPHTHOROMYCETES
  • ORDER ENTOMOPHTHORALES
    • Entomophthora, Condiobolus, Completoria, Meristacrum, Neozygites.

• CLASS ZOOPAGOMYCETES
  • ORDER ZOOPAGALES
    • Zoopage, Amoebophilus, Piptocephalis, Rhopalomyces, Sigmoideomyces, Stylopage, Syncephalis, Chochlonema.

• CLASS KICKXELLOMYCETES
  • ORDER KICKXELLALES
    • Dipsacomyes, Kickxella, Coemansia, Linderina, Martensella, Martensiomyces, Spirodactylon, Spiromyces.
  • ORDER DIMARGARITALES
    • Dimargaris, Dispira, Spinalia, Tieghemiomyces.
  • ORDER HARPELLALES (SMITTALES)
    • Smittum, Furculomyces, Legeriomyces, Harpella, Enterobryus, Orphella, Zygopolaris.
  • ORDER ASELLARIALES
    • Asellaria, Orchesellaria

• INCERTAE SEDIS
  • ORDER BASIDIOBOLALES
    • Basidiobolus.

PHYLUM EUZYGOMYCOTA

• CLASS MUCOROMYCETES
  • ORDER MUCORALES
    • Mucor, Rhizopus, Pilobolus, Chaetocladium, Choanephora, Phycomyces, Syncephalestrum, Thamnidium.
  • ORDER ENDOGONIALES
    • Densospora, Endogone, Pteridiospora, Sclerogone, Youngiomyces.
  • ORDER MORTIERELLALES
    • Mortierella, Dissiphora, Modicella.

PHYLUM GLOMEROMYCOTA

• CLASS GLOMEROMYCETES
  • ORDER ARCHAESPORALES
    • Archaespora, Geosiphon.
  • ORDER DIVERSISPORALES
    • Acaulospora, Diversispora, Gigaspora, Pacispora (and some species of Glomus).
  • ORDER GLOMERALES
    • Glomus
  • ORDER PARAGLOMERALES
    • Paraglomus.