Studies of species composition of extinct and contemporary small mammals faunas in combination with spore and pollen analysis, and data on malacofaunas and ostracods, shed light on the origins of contemporary ecosystems of the Middle and South Trans-Urals. Differences between the two regional ecosystems, of the beginning of the Late Pliocene in the South Trans-Urals, and the late Middle Pleistocene in the Middle Trans-Urals are defined, although they were less substantial than that of the modern ecosystems. Autochthonous and allochthonous components of modern fauna of these regions are recognized. Copyright © 1997 by MAK Haya/Interperiodica Publishing.