• Agmasoma penaei (Sprague) E.I. Hazard & Oldacre, 1975
• Desmozoon lepeophtherii Freeman & Sommerville, 2009
• Enterocytozoon hepatopenaei Tourtip, Wongtripop, Situnyalucksana, Stentiford, Bateman, Sriuratana, Chayaburakul & Withyachumnarkul, 2009
• Enterocytozoon salmonis Hedrick, Groff & Baxa, 1991
• Enterospora canceri Stentiford, Bateman, Longshaw & Feist, 2007
• Hrabyeia xerkophora J. Lom & I. Dykova, 1990
• Jirovecia piscicola (Cépède, 1924)
• Mrazekia piscicola Cépède, 1924 accepted as Jirovecia piscicola (Cépède, 1924)
• Nosema bengalis Weiser, Kalavati & Sandeep, 1981 accepted as Microsporidium bengalis (Weiser, Kalavati & Sandeep, 1981)
• Nosema ceratomyxae Diamant & Paperna, 1985
• Nosema cotti Chatton & Courier, 1923 accepted as Microsporidium cotti (Chatton & Courrier, 1923)
• Nosema dollfusi
• Nosema legeri Dollfus, 1912 accepted as Unikaryon legeri (Dollfus, 1912)
• Nosema locustae Canning, 1953
• Nosema marionis (Thélohan, 1895) Labbé, 1899
• Nosema michaeli
• Nosema necatrix Kramer, 1965
• Nosema notabilis Kudo, 1939
• Nosema ormieresi Comps, Pichot & Deltreil, 1979
• Nosema ovoideum (Thélohan, 1895) Labbé, 1899 accepted as Microgemma ovoidea (Thélohan, 1895) Amigo, Salvado, Gracia & Vivares, 1996
• Nosema sauridae Narasimhamurti & Kalavati, 1972 accepted as Microsporidium sauridae
• Nosema spelotremae Guyénot, Naville & Ponse, 1925 accepted as Unikaryon spelotremae (Guyénot, Naville & Ponse, 1925)
• Nosema tisae Lom & Weiser, 1969
• Nosema trichoplusiae Tanabe & Tamashiro, 1967
• Nosema valamugili Kalavati & Lakshminrayana, 1892 accepted as Microsporidium valamugili (Kalavati & Lakshminrayana, 1892)
• Nucleospora salmonis (Hedrick, Groff & Baxa, 1991)
• Nucleospora seconda Lom & Dykoá, 2002
• Paranucleospora theridion Nylund, Nylund, Watanabe, Arnesen & Kalrsbakk, 2010 accepted as Desmozoon lepeophtherii Freeman & Sommerville, 2009