Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE Huhndorg S, James T, Kirk PM, Lucking R, Lumbsch T, Lutzoni F, Matheny PB, McLaughlin D, Powell MJ, Redhead S, Schoch CL, Spatafora JW, Stalpers JA, Vilgalys R, Aime CA, Aptroot A, Bauer R, Begerow D, Benny GL, Castlebury LA, Crous PW, Dai Y-C, Gams W, Geiser DM, Griffith GW, Gueidan C, Hawksworth DL, Hestmark G, Hosaka K, Humber RA, Hyde K, Ironside JE, Koljalg U, Kurtzman CP, Larrson K-H, Lichtwardt R, Longcore J, Mia Klikowska J, Miller A, Moncalvo J-M, Mozley-Standridge S, Oberwinkler F, Parmasto E, Reeb V, Rodgers JD, Roux C, Ryvarden L, Sampaio JP< Schussler A, Sugiyama J, Thorn RG, Tibell L, Untereiner WA, Walker C, Wang Z, Weir A, Weiss M, White MM, Winka K, Yao Y-J, Zhang N. 2007. A higher-level phylogenetic classification of the Fungi. Mycological Research 111: 509-547.

Results of Liu et al. (2006) supported the monophyly of the traditional Zygomycota (Mucorales, Glomerales, Entomophthorales, and Harpellales) but James et al. (2006), which included broader sampling and additional molecular loci, found Zygomycota to be polyphyletic. Until the basal fungal lineages are more clearly resolved the traditional groups of Zygomycota have been broken up and placed into distinct subphyla (Hibbett et al. 2007).

James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox C, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold EA, Amtoft A, Stajich JE, Hosaka K, Sung G-H, Johnson D, O'Rourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schler A, Longcore JE, O'Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton J, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lcking R, Bdel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin D, Spatafora J, Vilgalys R, 2006. Reconstructing the early evolution of the fungi using a six gene phylogeny. Nature 443: 818-822.

Liu YJ, Hodson MC, Hall BD, 2006. Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of kingdom Fungi inferred from RNA polymerase II subunit genes. BMC Evolutionary Biology 6: 74.

Tanabe Y, Saikawa M, Watanabe MM, Sugiyama J. Molecular phylogeny of Zygomycota based on EF-1alpha and RPB1 sequences: limitations and utility of alternative markers to rDNA. (Mol Phylogenet Evol. 30: 438-449, 2004)

Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A, James TY, O'Donnell K, Roberson RW, Taylor TN, Uehling J, Vilgalys R, White MM, Stajich JE. 2016. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia. 108: 1028-1046.