The Caspian turtle (Mauremys caspica), although found in neighboring areas, is a wholly freshwater species. The zebra mussel is native to the Caspian and Black Sea basins, but has become an invasive species elsewhere, when introduced. The area has given its name to several species, including the Caspian gull and the Caspian tern. The Caspian seal (Pusa caspica) is the only aquatic mammal endemic to the Caspian Sea, being one of very few seal species that live in inland waters, but it is different from those inhabiting freshwaters due to the hydrological environment of the sea. A century ago the Caspian was home to more than one million seals. Today, fewer than 10% remain.
Archeological studies of Gobustan Rock Art have identified what may be oceanic species including cetaceans from baleen whales to dolphins, and auks most likely Brunnich's Guillemot, although the rock art on Kichikdash Mountain which is assumed to depict either a beaked whale or a dolphin, it may represent the famous beluga sturgeon instead due to its size (430 cm in length).  These petroglyphs may suggest potential presences of oceanic faunas in the Caspian Sea presumably until the Quaternary or even the last glacial period or antiquity due to historic marine inflow between the current Caspian Sea and either the Arctic Ocean or North Sea, or the Black Sea. This is supported by the existences of current endemic, oceanic species such as lagoon cockles which was genetically identified to originate in the Caspian and Black Seas regions.
The seas basin (including associated waters such as rivers) has 160 native species and subspecies of fish in more than 60 genera. About 62% of the species and subspecies are endemic, as are 4–6 genera (depending on taxonomic treatment). The lake proper has 115 natives, including 73 endemics (63.5%). Among the more than 50 genera in the lake proper, 3–4 are endemic: Anatirostrum, Caspiomyzon, Chasar (often included in Ponticola) and Hyrcanogobius. By far the most numerous families in the lake proper are gobies (35 species and subspecies), cyprinids (32) and clupeids (22). Two particularly rich genera are Alosa with 18 endemic species/subspecies and Benthophilus with 16 endemic species. Other examples of endemics are four species of Clupeonella, Gobio volgensis, two Rutilus, three Sabanejewia, Stenodus leucichthys, two Salmo, two Mesogobius and three Neogobius'. Most non-endemic natives are either shared with the Black Sea basin or widespread Palearctic species such as crucian carp, Prussian carp, common carp, common bream, common bleak, asp, white bream, sunbleak, common dace, common roach, common rudd, European chub, sichel, tench, European weatherfish, wels catfish, northern pike, burbot, European perch and zander. Almost 30 non-indigenous, introduced fish species have been reported from the Caspian Sea, but only a few have become established.
Six sturgeon species, the Russian, bastard, Persian, sterlet, starry and beluga, are native to the Caspian Sea. The last of these is arguably the largest freshwater fish in the world. The sturgeon yield roe (eggs) that are processed into caviar. Overfishing has depleted a number of the historic fisheries. In recent years, overfishing has threatened the sturgeon population to the point that environmentalists advocate banning sturgeon fishing completely until the population recovers. The high price of sturgeon caviar – more than 1,500 Azerbaijani manats (US$880 ) per kilo – allows fishermen to afford bribes to ensure the authorities look the other way, making regulations in many locations ineffective. Caviar harvesting further endangers the fish stocks, since it targets reproductive females.
Reptiles native to the region include the spur-thighed tortoise (Testudo graeca buxtoni) and Horsfield's tortoise.
*The Asiatic cheetah used to occur in the Trans-Caucasus and Central Asia, but is today restricted to Iran.
*The Asiatic lion used to occur in the Trans-Caucasus, Iran, and possibly the southern part of Turkestan.
*The Caspian tiger used to occur in northern Iran, the Caucasus and Central Asia.
*The endangered Persian leopard is found in Iran, the Caucasus and Central Asia.