Of the 17,500 vertebrate and invertebrate species recorded in the country, 329 are endemic to Armenia. These include a wide range of invertebrates (including Phytodrymadusa armeniaca, Nocarodes armenus, Olophrum aragatzense, Amphycoma eichleri, Cantharis araxicola, Tomomyza araxana, Bombilius schelkovnikovi, Shadinia akramowskii, and Gabbiella araxena), as well as a number of vertebrate species and sub-species.

Nine species and sub-species of fish are endemic to Armenia. These include the endemic species of Sevan trout (Salmo isshkhan), and its four races or sub-species (winter bakhtak S. ischchan; gegharkuni S. ischchan gegarkuni; bojak S. ischchan danilewskii; and summer bakhtak S. ischchan aestivalis), which occur in Lake Sevan and surrounding rivers. In addition, the following sub-species of fish are also endemic to Armenia, a roach (Armenian karmrakn, Rutilus rutilus schelkovnikovi); a schneider species (Armenian tarekhik, Alburnoides bipunctatus armeniensis); Sevan koghak (Varicorhinus capoeta sevangi); a barbel (Sevan beghlou Barbus lacerta goktschaicus); and a white bream species (Armenian goustera (Blicca bjoerkna derjavini).

Populations of trout (Salmo trutta), which until recently was found in all rivers in Armenia and Wels catfish (Silurus glanis) have reduced significantly as a direct result of human activities such as intensive poaching, reservoir pollution, unlimited water use and uncontrolled fishing.

Of the 53 reptile species found in Armenia, over 13% are endemic. These include several species of rock lizards including Lacerta unisexualis (white-bellied lizard, found in the Sevan basin, and surrounding areas), L. armeniaca (the Armenian lizard, found in the north of the country), and L. nairensis (found around Hrazdan river and Lake Sevan). Other endemic species and sub-species include Eremias arguta transcaucasica (the racerunner, from Lake Sevan basin), Vipera darevskii (Darevsky's viper, from Djavakhk mountain range at 2000-3000 m), and V. raddei (Armenian viper, from Armenian Plateau and Minor Caucasus). Regional endemics (restricted to the Armenian plateau) include several rock lizards (Lacerta dahli, L. rostombekovi and L. valentini). In addition, one amphibian, the Syrian spadefoot toad (Pelobates syriacus), is endemic to the country.

No true endemic bird species are found in Armenia, although the Armenian gull (Larus armenicus) is considered to be an endemic species, and has been recorded in the Lake Sevan basin, along the Arax, Hrazdan, and Akhurian rivers, and in recent years in the Ararat valley. In addition, the Caucasian grouse (Tetrao mlokosiewiczi), which is endemic to the Caucasus, is uncommon in Armenia.
Among 83 mammals recorded in Armenia, six endemic species or sub-species are recorded - the northern mole vole (Ellobius lutescens), Vigradov's jird (Meriones vinogradovi), a jeroboa (Allactaga williamsi), the Caucasian birch mouse (Sicista caucasica), the Armenian mouflon (Ovis orientalis gmelinii), and a sub-species of Natterer's bat (Myotis nattereri araxenus). Of particular note is the Armenian mouflon which is now restricted to areas in southern Armenia.

Few relict animal species have been recorded from Armenia. One sub-species of fish, a roach ('Armenian karmrakn', Rutilus rutilus schelkovnikovi) appears to be a relict of Tertiary origin, which has been preserved within the Metsamor basin. Two birds, the white-winged scoter (Melanitta fusca) and the boreal owl (Aegolius funereus), are also considered to be relict species.

A number of vertebrate species are listed in the Red Data Book for Armenia, and many more are now considered to be undergoing decline. Studies of around 316 endemic species and sub-species, have revealed that around 100 of these are rare or declining.

Among the vertebrates species of key concern include a number of sub-species of fish, which have been threatened by declines in the water level of Lake Sevan and by over-fishing. For example, 'winter bakhtak' (Salmo ischchan), which previously made up 30% of Sevan trout stocks, has now practically disappeared, while 'bojak' (S. ischchan danilewskii) is also rarely found now. Spawning of 'summer bakhtak' (S. ischchan aestivalis) has been disrupted by both the decline in the level of Lake Sevan, and the damming of rivers, leading to declines in this sub-species, while populations of 'gegharkuni' (S. ishkhan gegarkuni) are currently maintained through artificial breeding. 'Sevan beghlou' (Barbus lacerta goktschaicus) declined following the changes in Lake Sevan (leading to habitat loss) and this species is now listed in the Red Data Book of Armenia.

Many Armenian reptiles are threatened (including a number of endemics and regional endemics). Threatened species include the Caucasian rat snake (Elaphe hohenackeri), Armenian viper (Vipera raddei), and a lidless skink (Ablepharus chernovi) among others. The population of the racerunner (Eremias arguta transcaucasica) numbering 100 individuals, in the Sevan basin, is the only one in the Caucasus. A number of semi-desert and alpine bird species are considered threatened, vulnerable or extinct, while status of others has not yet been determined. Research many of these species is limited, but such birds appear to be under increasing threat. Among mammals, the distribution and population of Armenian mouflon (Ovis orientalis gmelinii) have declined as a result of habitat loss and poaching. This species has undergone a significant range reduction during the last 20 years, when it has disappeared from the Ararat Valley, and is now restricted to sites in southern Armenia (Khosrov Reserve and adjacent areas).