The rich and interesting fauna of the Mljet National Park has not yet been fully researched. One of the peculiarities of the island are the typical karst underground habitats, caves and pits, with an endemic fauna of invertebrates which were first discovered at Mljet and have the name of the island in their official names, for example the cave snail Meledella werneri.

So far, five types of snakes and four types of lizards have been registered on the island. Regarding the  lizards, the most frequent are the sharp-snouted rock lizard (Dalmatolacerta oxycephala), the Dalmatian wall lizard (Podarcis melisellensis) and the Mediterranean house gecko (Hemidactylus turcicus). The population of snakes on the island has dwindled due to the introduction of the small Asian mongoose (Herpestes auropunctatus) in 1910.

The sharp-snouted rock lizard has a lead blue dark grey upper part of the body in various shades with black stripes. The lower part of the body is a single colour blue-grey, and completely blue in the neck area. It grows up to 20 cm in length. It lives in barren and rocky areas where it hides in crevices and under rocks. It is very frequently found on stone walls and fences, walls and roofs of houses in settlements where it frequently resides and moves with great dexterity.

The Dalmatian wall lizard grows up to 6.5 cm, but can be significantly smaller. The colours vary wildly. The basic colour is brown or green with dark and light stripes, sometimes with a web of stripes formed. Some populations and/or specimens have no stripes at all. These specimens have a single colour of brown-green. The belly is white, yellow or orange, usually without additional marks or spots. Some populations or specimens have blue dots on the edge of the outside row of the abdominal muscles.

The Mediterranean house gecko is an exclusively nocturnal animal. It has a slender 8 – 10 cm long body, white on the lower side, and pinkish with brown spots on the upper side with a large number of warts. It has large eyes with vertical slit pupils, but no eyelids. Instead, it has a transparent membrane covering its eyes, and it cleans this membrane with its tongue. The house geckoes produce a special type of sound similar to loud croaking.

Mljet is located in the migration path of birds, and is therefore an important habitat for birds to rest and feed at. 119 species have been recorded so far in the wider area of the Park, with 52 nesting birds. The most important species for the Park are the European shag (Phalacrocorax aristotelis), Audouin’s gull (Larus audouinii), common tern (Sterna hirundo), European honey buzzard (Pernis apivorus) and Peregrine falcon (Falco peregrinus). Audouin’s gull is the most endangered species of gulls in Croatia and one of the nesting birds with the lowest populations. The nesting population of the European honey buzzard has been marked as vulnerable (VU), and Mljet is the only know nesting ground for this species in Dalmatia. The European honey buzzard and the tawny owl (Strix aluco) nest in the forests of Mljet, which is rare on other Adriatic islands. Mljet is also the nesting ground for the rare Eurasian eagle-owl (Bubo bubo). 90 bird species recorded so far in the Park area are strictly protected species in Croatia

There are 26 species of mammals in the Park. The fallow deer (Dama dama), the chital (Axis axis), mouflon (Ovis (orientalis)musimori) and the wild boar (Sus scrofa) are introduced species, as is the small Asian mongoose (Herpestes javanicus auropunctatus). There are 10 species of bats, with the endangered species of common bent-wing bat (Miniopterus schreibersi) among them, and all species are strictly protected by law