Protected species of Estonia, category II
| Taxon name | Common name |
|---|---|
| Accipiter gentilis | Northern Goshawk |
| Aegolius funereus | Tengmalm's Owl |
| Agrimonia pilosa | |
| Ajuga pyramidalis | |
| Ajuga reptans | |
| Alca torda | Razorbill |
| Alcedo atthis | Common Kingfisher |
| Alectoria sarmentosa | |
| Alisma gramineum | |
| Allium vineale | |
| Amanita friabilis | |
| Anacamptis pyramidalis | |
| Anas acuta | Northern Pintail |
| Angelica palustris | |
| Anomodon rugelii | |
| Anthus campestris | Tawny Pipit |
| Anthus petrosus | Eurasian Rock Pipit |
| Arctium nemorosum | |
| Arenaria interpres | Ruddy Turnstone |
| Arenaria procera | |
| Artemisia maritima | |
| Asio flammeus | Short-eared Owl |
| Asplenium ruta-muraria | |
| Asplenium trichomanes | |
| Aythya marila | Greater Scaup |
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