Dense broadleaf forests of local forests marked by rocky massifs, rapid streams, deep canyons, humid glades and steep slopes provide sufficient habitats for such mammals as the brown bear (Ursus arctos), Eurasian lynx (Lynx lynx), European wildcat (Felis silvestris silvestris), European roe dear (Capreolus capreolus), wild boar (Sus scrofa), gray wolf (Canis lupus), red fox (Vulpes vulpes), European badger (Meles meles) and European hare (Lepus europaeus). The Indian porcupine (Hystrix indica) and long-eared hedgehog (Hemiechinus auritus) included to the Red Data Book of Armenia are recorded quite frequently in the reserve.
The common dwellers of local forests and open dry slopes are common vole (Microtus arvalis), least weasel (Mustela nivalis), stone marten (Martes foina) and Eastern European hedgehog (Erinaceus concolor).
The areas lying near the treeline and along the ridgetops are inhabited by rare European lynx and endangered Caucasian leopards (Panthera pardus ciscaucasica), both of which are listed in the IUCN Red List of Threatened Species.
The leopard movement routes pass through the Meghri Ridge watershed, i.e. the upper parts of the boundary of Shikahogh State Reserve and Arevik National Park. Deep canyons and precipitous slopes covered by sparse forests and arid grasslands with rocky massifs are the leopard’s preferred habitats.
Another species occurring in the reserve is the bezoar goat (Capra aegagrus) which is spatially confined to the steep rocky slopes protruding through the forest and scattered along the treeline. The Armenian mouflon (Ovis orientalis gmelinii) lived before in subalpine meadows of the reserve, but at present is surviving in Zangezur State Sanctuary alone. Both these ungulates are registered in the IUCN Red List of Threatened Species.
The bats living in the reserve comprise the Monticelli’s myotis (Myotis oxygnathus), lesser horseshoe bat (Rhinolophus hipposideros), common pipistrelle (Pippisrellus pipistrellus), Natterer’s bat (Myotis nattereri), Kuhl’s pipistrelle (Pipistrellus kuhli) and Schaub’s myotis (Myotis schaubi araxenus), included to the Red Data Book of Armenia.
Ornithofauna is represented by 141 species mostly forest-dwelling ones. The Caspian snowcock (Tetraogalus caspius), Caucasian black grouse (Tetrao mlokosiewiczi) and lammergeier (Gypeatus barbatus) are the most eye-catching and the rarest species listed in the Red Data Book of Armenia. The griffon vulture (Gyps fulvus) occurs towards the upper limits of the forest.
The common pheasant (Phasianus colchicus), black francolin (Francolinus francolinus), Kurdish wheatear (Oenanthe xanthoprymna) and others, in total more than 50 species, have limited distribution.
The gallinaceous birds include 4 species. The Caspian snowcock (Tetraogalius caspius) inhabits the fringes of rocky massifs and cliffs, in quite small numbers. The gray partridge (Perdix perdix) is widespread in forest grasslands and shrubs. Chukars (Alectoris chukar) are common in semideserts, mountain grasslands and rocky areas of meadows. The quail (Cotumix cotumix) lives in high-grass meadows.
The common and black redstarts, hoopoe bluethroat and trule dove are common and widespread in the reserve, whereas the laughing dove, common stonechat, isabelline wheatear, little owl, scops owl, long-eared owl and others are rarer.
The reptiles are 26 species, including 11 lizards 13 snakes and 2 tortoises. The Schneider’s skink (Eumeces schneideri), Asia minor mabuya (Trachylepis septemtaeniata), cat snake (Telescopus fallax) and Transcaucasian rat snake (Zamenis hohenackeri) are listed in the Red Data Book of Armenia. The Armenian viper (Montivipera raddei) living in xerophilic forests and mountain grasslands and the spur-thighed tortoise (Testudo graeca) from foothills are also registered in the IUCN Red List of Threatened Species.
The Caucasian agama (Laudakia caucasia) Radde’s lizard (Darevskia raddei), Caspian green lizard (Lacerta strigata) and three-lined lizard (Lacerta media) are common in arid foothills and rocky habitats. The European glass lizard (Pseudopus apodus), European blind snake (Typhlops vermicularis), collared dwarf snake (Eirenis collaris), dotted dwarf snake (Eirenis punctatolineatus), Hidrophis schimidti and Eurasian sand boa (Eryx jaculus) live in arid grasslands, sparse forests and thickets. The grass snake (Natrix natrix) and dice snake (Natrix tesselata) are associated with riparian habitats. The two-streaked snake-eyed skink (Ablepharus bivittatus) inhabits rocky foothills with clayey substrates and the slow worm (Anguis fragilis) occurs in broadleaf mixed forests and glades. The spotted whip snake (Hemorrhois ravergieri) and blotched snake (Elaphe sauromates) are distributed in rocky areas over higher parts of the forest and in mountain grassland. The Lebetine viper (Macrovipera lebetina), Armenia’s most venomous snake, is found almost everywhere.
Some areas located in mountain grassland at elevations 2100-2300 m are co-inhabited by species from different landscapes, e.g. Armenian viper, Lebetine viper, blotched snake and others. This issue deserves further research to elucidate the species adaptability to environmental conditions.
The reserve holds 4 species of amphibians. The marsh frog (Rana ridibunda) and green toad (Bufo viridis) are widespread in local wetlands. The long-legged wood frog (Rana macrocnemis) occurs in some rapid streams at higher elevations. The tree frog (Hyla savignyi) is rather uncommon.