The article focuses on modeling tectonic zonality of the sedimentation cover in the Black Sea-Caspian Region, and addresses the identification and validation of the Late Paleozoic, Mesozoic, Alpine and recent-time geodynamically active structures. The modeling shows that the significant events, which governed the evolution features of the geodynamically active structures, correlate with the recent time. That is the time when such sedimentation basins as Terek-Caspian, Indol-Kuban, Eastern Kuban and Karkinit have finally set. The first three basins in this list occur in the zones of the reverse geodynamic regime, with dominant extension and downwarping within the limits of cratons, and belong to the Black Sea-Caspian geodynamically active structure. The Karkinit basis belongs to the Scythian geodynamically active structure with generally compressive tectonics, dominant upheaval or relative stabilization. The tectonic features have had the critical influence on both formation of the sedimentation cover of the basins and spatial distribution of minerals.