子囊菌门是一类较高等的真菌，可分成以下三个[[亚门]]：
* [[外囊菌亚门]] (Taphrinomycotina)
** [[粒毛盘菌纲]] Neolectomycetes** [[肺孢子菌纲]] Pneumocystidomycetes** [[裂殖酵母纲]] Schizosaccharomycetes** [[外囊菌纲]] Taphrinomycetes
* [[酵母亚门]] (Saccharomycotina)
** [[酵母纲]] ''Saccharomycetes''
* [[盘菌亚门]] (Pezizomycotina)
** [[星裂菌纲]] ''Arthoniomycetes''** [[座囊菌纲]] ''Dothideomycetes''** [[散囊菌纲]] ''Eurotiomycetes''** [[虫囊菌纲]] ''Laboulbeniomycetes''** [[茶渍纲]] ''Lecanoromycetes''** [[锤舌菌纲]] ''Leotiomycetes''** [[李基那地衣纲]] ''Lichinomycetes''** [[圆盘菌纲]] ''Orbiliomycetes''** [[盘菌纲]] ''Pezizomycetes''** [[粪壳菌纲]] ''Sordariomycetes''** [[刺盾炱纲]] ''Chaetothyriomycetes''
[[Category:子囊菌门| ]] [[Category:植物病原体]]
