The stone history of the mountainous nature of Tajikistan is well-exposed and easily accessible to study. There are numerous deposits of fossil fauna and flora, tens of which are unique; however, none of these is protected by the state. Some of the easily accessible deposits of fossils are now under the threat of destruction due to human activity.

Identification of the logic of the origin, development and extinction of ancient biosystems allows to learn more about the present biodiversity, reasons for survival, vulnerability, fragility and instability, and to work out the best solutions on species conservation.

Precambrian (more than 570 m.y.) fossils are rare in Tajikistan; they are represented by the remnants of primitive algae and rare invertebrates.

The oldest precise age of fossils found in Tajikistan is Paleozoic (570-230 m.y. ago). The Paleozoic organic world of Tajikistan is rich in composition. The territory of Paleozoic Tajikistan was occupied by tropical sea. At the end of Paleozoic, the total area of the present Northern, Central, and, partly, Eastern Tajikistan was free of water. That was the age when spore-bearing and gymnosperm plants developed. All classes of cold-blooded vertebrates (agnathous, fish, amphibian, and reptiles) appeared in Paleozoic. The invertebrates of the Paleozoic were represented by conodonts, brachiopods, rugoses, and tabulates; the first half of Paleozoic - by trilobites, archaeocyathids, graptolites, tentaculites, nautiloids, and endoceratites; in the second half of Paleozoic, goniatites and foraminifers were common. Peaks of sea invertebrate biodiversity were in Late Cambrian, Middle Ordovician, Early Devonian, Early Carboniferous, and Early Permian. Paleozoic fossils are found in numerous deposits of Tien Shan and the Pamirs.

By the beginning of Mesozoic (230-67 m.y. ago), the northern, Northeastern, Central, and a part of Southern Tajikistan was occupied by land, with young mountains; the Southern Tajikistan was a sea bottom. In Mesozoic, gymnosperms and filices dominated here. In the second half of Cretaceous, higher angiosperms were dominating. Of vertebrates, reptiles were common. Warm-blooded animals - mammals and birds - also appeared in Mesozoic. Invertebrates of Tajikistan were widely represented by ammonoids, bivalves (oysters, rudists); in early Mesozoic - by conodonts, in late Mesozoic - by echinoids. Peaks of sea invertebrate biodiversity were reached in Late Triassic, Middle Jurassic, and Middle Cretaceous. The Mesozoic fossils of Tajikistan were defined from numerous deposits of Tien Shan and the Pamirs.

In the Cainozoic era (for 67 m.y. till now), including the present stage of evolution, the alpine epoch of folding and mountain-formation that shaped the present appearance of mountains manifested itself. This epoch still continues on the territory of in the country. In the late Early Cainozoic, the sea completely regressed from the territory of Tajikistan and a continental regime was established everywhere in the country. Cainozoic is the time when all present families and genera of animals and plants appeared. A specific feature of the Cainosoic era is domination of higher angiosperms. Higher placental mammals that were common on Earth as early as the beginning of the era, develop; they inhabited land and accommodated to life in water and on land.

The localities of Cainosoic fossils and archaeological monuments are in the Kuramin, Turkestan, Zeravshan, Hissar, Karategin, Peter the Great, Zaalay, and Darvaz ridges; in the Fergana, Maghian, and Tajik depressions; and in the Pamirs.

Mass extinction of higher plant groups, as a rule, does not coincide with that of animals, it occurred approximately half geological era earlier