Koufonisi is an important place for dozens of migratory bird species that come here to rest and find food. As for the breeding species, we can find the common yellow-legged gull (Larus cacchinans), but also other sea birds such as Cory's shearwater (Calonectris diomedea), shearwater (Puffinus yelkouan), shag (phalacrocorax aristotelis desmarestii) and some raptors such as long-legged buzzard (Buteo rufinus), peregrine falcon (Falco peregrinus) and Eleonor’s falcon (Falco eleonorae).
Other animals include the lizard Podarcis erhardi cretensis, which basks on the white rocks and the Mediterranean monk seal (Monachus - monachus) which sometimes appears in the sea caves.