Over 100 bird species have been catalogued in the park, among them many raptors like golden eagles, short-toed eagles, booted eagles, Egyptian vultures, peregrines, kestrels and eagle owls. In the cultivated fields are hoopoes, crested larks and red-legged partridges. Woodpeckers and turtle doves are in the wooded areas. Badgers, genets, beech martens, wild cats and foxes are the most common among the 30 species of mammals inhabiting the park. The park is rich in game, like roe deer and wild boars. There are 17 species of reptiles and eight of amphibians, many of which can be found along the park's watercourses, including water snakes, southern toads, painted toads and painted frogs. Unique to the Hoya de Baza region is the Baza butterfly (eucloe bazae).
The park was designated a bird protection area (ZEPA) in 2002 for its outstanding ornithological interest. Nesting on the limestone cliff faces in the park are Egyptian vultures, Griffon vultures and peregrine falcons. Other raptors inhabit the pine and holm oak woodland areas, such as short-toed, golden and booted eagles. The rivers and the trees lining their banks are home to grey herons, wagtails, kingfishers and dippers, while in the water itself are otters and trout. Mountain goats, muflon, wild boar, fallow deer and martens are the main mammals, although there is speculation on the presence of the threatened Iberian lynx. There are many butterflies endemic to the Iberian peninsula. Due to its numerous watercourses, the park is rich in reptiles and amphibians, many of which are rare elsewhere. It is the only place in Spain apart from Jaen and Albacete provinces where the Spanish algyroides, also known as Valverde's lizard, can be found and the park also has painted frogs, southern midwife toads, Lataste's vipers, salamanders and grass snakes.
The park has many birds of prey, among them are golden, short-toed and Bonelli's eagles, buzzards, kestrels and goshawks. It has one of Andalucia's largest colonies of griffon vultures, with around 100 pairs, and one of the Sierra's Morena's most important populations of black vultures, with 50 pairs. The three reservoirs in the park - Bembézar, Breña and Retortillo - are popular with numerous great comorants in winter. Mammals include Egyptian mongeese, genets, wild boars and red deer, as well as otters in the reservoirs and rivers.