The territory of Sitia, due to its unique geographic location, is home to a large number of characteristic animals of the island, especially migratory birds. Twenty of the bird species that have been sighted in the area (migratory, indigenous) are in the Red Data Book of Threatened Vertebrates of Greece.

Birds visitors can observe in coastal areas are the Little Egret (Egretta garzetta), Cory’s Shearwater (Colonectris diomedea), the European Shag (Phalacrocorax aristotelis), (the European Storm Petrel), the Western Marsh Harrier (Circus aeruginosus), Audouin’s Gull (Larus audiouinii) and the Woodchat Shrike (Lanius sanator sanator). Of the predatory and scavenger birds, the most characteristic are Eleonora’s Falcon (Falco eleonorae), the Golden Eagle (Aquila chrysaetos), the Peregrine Falcon (Falco peregrinus), the Common Buzzard (Buteo buteo), the Lesser Kestrel (Falco naumanni), the Griffon Vulture (Gyps fulvus) and the Bearded Vulture (Gypaetus barbatus). The Bearded Vulture occasionally makes an appearance in the area and it is one of the most important species on the island as the Cretan population is the only reproducing population in all the Balkans.

As far as mammals are concerned, 14 species have been recorded in the Park area, four of which are cetaceans, like the strictly protected Bottlenose Dolphin (Tursiops truncatus), and the Mediterranean Monk Seal (Monachus monachus), the Striped Dolphin (Stenella coruleoalba) and the Common Dolphin (Delphinus delphis). Of the land mammals the most characteristic is the European Hare, the Least Weasel, the Beech Marten, the European Badger, and the Spiny Mouse, while in caves there are Pipistrellus savii bats, a strictly protected species.

Many of the eight species of reptiles and two of the three species of amphibians of the region are included in Directive 92/43 EEC and the Berne Convention. In this area all three species of amphibians found in Crete may be encountered, namely the European Green Toad (Bufo viridis), the Common Tree Frog (Hyla arborea cretensis), an indigenous species to Crete and the only species of tree frog in Europe, and the Marsh Frog (Rama ridibunda).

One of the most important reptiles of the area is the Caspian Turtle (Mauremis caspica), the only species of water turtle on Crete that can be observed in streams in the palm forest of Vai, in the canyon at Toplou Monastery and, mainly, in Kato Zakros. Furthermore, the Caretta caretta sea turtle breeds on the sandy beaches of the Vai palm forest, in Kouremenos and in Xerokambos. Very important to the area are the Podarcis cretensis lizards, which are the only indigenous lizard species on the island, and the Ocellated Skink (Chalcides ocellatus), which is found in Italy, Greece and North Africa, and which is mistakenly considered poisonous on Crete.

Of the snakes in the area none are dangerous to humans. The Balkan Whip Snake (Coluber gemonensis) and the European Rat Snake (Elaphe situla), the most beautiful snake in Greece, are completely harmless to humans, while the European Cat Snake is the only snake on the island with venom, which, however, is very weak and secreted from its back teeth, a fact that renders it virtually harmless.