List of species and infraspecific taxa
- Species: Puttea caesia (Fr.) M. Svenss. & T. Sprib.
- Remark: earlier under Lecidea symmictella
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Lichenothelia rugosa (G. Thor) Ertz & Diederich
- Remark: earlier under Lichenostigma rugosum
- Fungus type: lichenicolous
- Treatment in Estonia: certain
- Species: Cetrariella commixta (Nyl.) A. Thell & Kärnefelt
- Remark: earlier under Melanelia commixta
- Fungus type: lichenized
- Treatment in Estonia: certain
- kivi-pruunsamblik
- Species: Halospora discrepans (J.Lahm ex Arnold) Hafellner
- Remark: earlier under Merismatium discrepans
- Fungus type: lichenicolous
- Treatment in Estonia: doubtful
- Species: Capronia triseptata (Diederich) Etayo
- Remark: earlier under Muellerella triseptata
- Fungus type: lichenicolous
- Treatment in Estonia: doubtful
- Species: Didymocyrtis peltigerae (Fuckel) Hafellner
- Remark: earlier under Polycoccum peltigerae
- Fungus type: lichenicolous
- Treatment in Estonia: certain
- Species: Ramboldia cinnabarina (Sommerf.) Kalb, Lumbsch & Elix
- Remark: earlier under Pyrrhospora cinnabarina
- Fungus type: lichenized
- Treatment in Estonia: doubtful extinct
- Species: Kuettlingeria erythrocarpa (Pers.) I.V. Frolov, Vondrák & Arup
- Remark: earlier under Caloplaca erythrocarpa; also wrongly identified as Rufoplaca arenaria
- Fungus type: lichenized
- Treatment in Estonia: doubtful extinct
- Species: Nesothele hymenogonia (Nyl.) Orange
- Remark: earlier under Staurothele hymenogonia
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Endococcus hafellneri (Zhurb.) Zhurb.
- Remark: earlier under Stigmidium hafellneri
- Fungus type: lichenicolous
- Treatment in Estonia: certain
- Species: Sphaerellothecium pumilum (Lettau) Nav.-Ros., Cl. Roux & Hafellner
- Remark: earlier under Stigmidium pumilum
- Fungus type: lichenicolous
- Treatment in Estonia: certain
- Species: Absconditella pauxilla Vězda & Vivant
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Aquacidia trachona (Ach.) Aptroot
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Arthonia helvola Nyl.
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Arthonia reniformis (Pers.) Röhl.
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Bryostigma phaeophyciae (Grube & Matzer) S.Y. Kondr. & Hur
- Remark:
- Fungus type: lichenicolous
- Treatment in Estonia: certain
- Species: Cladonia rubrotincta Vtípilová, Timdal, Resl & Steinová
- Remark: formerly treated as C. norvegica by Estonian authors
- Fungus type: lichenized
- Treatment in Estonia: certain
- punalaik-porosamblik
- Species: Endococcus verrucosus Hafellner
- Remark:
- Fungus type: lichenicolous
- Treatment in Estonia: certain
- Species: Everniicola flexispora D. Hawksw.
- Remark:
- Fungus type: lichenicolous
- Treatment in Estonia: certain
- Species: Lecidea fuliginosa Taylor
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Lempholemma chalazanum (Ach.) B. de Lesd.
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- pae-liistsamblik
- Species: Lepraria membranacea (Dicks.) Vain.
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Melaspilea bagliettoana Zahlbr.
- Remark:
- Fungus type: saprotrophic
- Treatment in Estonia: certain
- Species: Phaeophyscia hirsuta Essl.
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- karvane tõmmusamblik
- Species: Tetramelas pulverulentus (Anzi) A. Nordin & Tibell
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain