List of species and infraspecific taxa
- Species: Acrocordia gemmata (Ach.) A. Massal.
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- suur kühmsamblik
- Species: Acrocordia salweyi (Keight. Ex Nyl.) A.L. Sm.
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Adelococcus alpestris (Zopf) Zopf ex Arnold
- Remark:
- Fungus type: lichenicolous
- Treatment in Estonia: certain
- Species: Adelolecia kolaënsis (Nyl.) Hertel & Rambold
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Agonimia allobata (Stizenb.) P. James
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Agonimia gelatinosa (Ach.) M. Brand & Diederich
- Remark: earlier under Polyblastia gelatinosa (Ach.) Th. Fr.
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Agonimia globulifera M. Brand & Diederich
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Agonimia tristicula (Nyl.) Zahlbr.
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Alectoria sarmentosa (Ach.) Ach.
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- oksa-tuustsamblik
- Species: Amandinea cacuminum (Th. Fr.) H. Mayrhofer & Sheard
- Remark: earlier under Rinodina cacuminum (Th. Fr.) Malme
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Amandinea coniops (Wahlenb.) Scheid. & H. Mayrhofer
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Amandinea punctata (Hoffm.) Coppins & Scheid.
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Amygdalaria panaeola (Ach.) Hertel & Brodo
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain extinct
- Species: Anaptychia ciliaris (L.) Körb. var. ciliaris
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: synonym
- harilik ripssamblik
- Species: Anaptychia ciliaris var. melanosticta (Ach.) Boistel
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: synonym
- meri-ripssamblik
- Species: Anaptychia runcinata (With.) J.R. Laundon
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- tõmmu ripssamblik
- Species: Anisomeridium biforme (Borrer) R.C. Harris
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Anisomeridium polypori (Ellis & Everh.) M.E. Barr
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Arctoparmelia centrifuga (L.) Hale
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- sõõr-põhjasamblik
- Species: Arctoparmelia incurva (Pers.) Hale
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- pais-põhjasamblik
- Species: Arthonia apatetica (A. Massal.) Th. Fr.
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain
- Species: Arthonia byssacea (Weigel) Almq.
- Remark: see: Inoderma byssaceum (Weigel) Gray
- Fungus type: lichenized
- Treatment in Estonia: synonym
- rant-tähnsamblik
- Species: Arthonia caerulescens (Almq.) R. Sant.
- Remark:
- Fungus type: lichenicolous
- Treatment in Estonia: certain
- Species: Arthonia cinnabarina (DC.) Wallr.
- Remark: see: Coniocarpon cinnabarinum DC.
- Fungus type: lichenized
- Treatment in Estonia: synonym
- Species: Arthonia didyma Körb.
- Remark:
- Fungus type: lichenized
- Treatment in Estonia: certain