
These are species with at least one recorded territory in Estonia, not a national checklist: a bird list from eBird or Avibase is more complete. The counts follow recording effort as much as wildlife, so a country with more visitors and more naturalists will show more of both.
The species with the most open occurrence records in Estonia, among those a photograph exists for. Most recorded is not most numerous: it rewards animals that are common, conspicuous and live where people go.

Alces alces

Cervus elaphus

Sus scrofa

Capreolus capreolus

Eptesicus nilssonii

Crex crex

Haliaeetus albicilla

Nyctereutes procyonoides

Tetrastes bonasia

Luscinia luscinia

Tetrao urogallus

Branta leucopsis
The reference database has no regions filed under Estonia.
The field guide covers Estonia on the map, but none of its species have an entry written for them yet.