壺菌（英語：Chytridiomycota）是一類具有動孢子的真菌。其名稱來源於希臘文χυτρίδιον（chytridion），意思是「小壺」，因其產生動孢子的結構動孢子囊而得名。壺菌是真菌演化的過程中，最早分支出去的類群之一。具有幾丁質細胞壁和鞭毛。壺菌多為腐生，釋放酵素分解環境中的腐爛的有機物，再以滲透營養取得養分，也有一些壺菌寄生在別的生物中，例如造成兩生類壺菌病的蛙壺菌。[1]
下級分類
本門包括以下綱：
- 壺菌綱 Chytridiomycetes M. Möbius 1929
- Lobulomycetes
- Lobulomycetales
- Lobulomycetaceae
- Algomyces
- Alogomyces D.R.Simmons & Letcher, 2012
- Alogomyces tanneri D.R.Simmons & Letcher[2]
- Clydaea D.R.Simmons, 2009
- Cyclopsomyces
- Lobulomyces D.R.Simmons
- Maunachytrium D.R.Simmons, 2009
- Lobulomycetaceae
- Lobulomycetales
- Mesochytriomycetes
- 單毛菌綱 Monoblepharidomycetes J.H. Schaffn. 1909
- 單毛菌目 Monoblepharidales Sparrow 1942
- Gonapodyaceae H.E. Petersen ex P.M. Kirk, P.F. Cannon & J.C. David 2001
- 肋壺菌科 Harpochytriaceae
- 單毛菌科 Monoblepharidaceae Warm. 1884
- Oedogoniomycetaceae D.J.S. Barr 1990
- Telasphaerulaceae Longcore & T.Y. James 2017
- 單毛菌目 Monoblepharidales Sparrow 1942
- 根生壺菌綱 Rhizophydiomycetes
- 根生壺菌目 Rhizophydiales
- 綱的地位未定的目：
- Nephridiophagales
- 綱、目的地位未定的科：
- Lagenidiaceae
- Plasmodiophoraceae
- Quaeritorhizaceae
- 綱、目、科的地位未定的屬：
- Arborella Zebrowski, 1936
- Arthurella Zebrowski, 1936
- Asteronema V.B.A.Trevisan, 1845
- Brijax M. Krings & C.J. Harper 2020
- Conchyliastrum Zebrowski, 1936
- Cultoraquaticus Strullu-Derr. 2016
- Dodgella Zebrowski, 1936
- Globicultrix M.Krings, N.Dotzler & T.N.Taylor, 2009
- Grilletia Renault & C.E.Bertrand, 1885
- Illmanomyces M. Krings & T.N. Taylor 2014
- Myrmicinosporidium Hölldobler, 1933
- Nimbosphaera C.J. Harper & M. Krings 2019
- Oochytrium B.Renault, 1895
- Paramoeciella Zebrowski, 1936
- Perexiflasca
- Rhizophidites Daugherty, 1941
- Tenuicutites C.E.Bertrand, 1898
- Thalassochytrium Nyvall, Pedersén & Longcore, 1999
- Trewinomyces
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