The Caspian and Black Sea Basins represent a system of intracontinental water bodies (relicts of the Paratethys) that differ in their natural characteristics and paleogeographic development. Numerous studies on environmental evolution in the basins have been published to date. However, most paleogeographic issues in every basin of the region still need to be debated. The topic of the junction of the Caspian and Black Seas during MIS 5 is among them. The main objective of our study is to prove the existence of the intersection of the basins in MIS 5. We studied the cores of four boreholes in the North Caspian, four boreholes in the Manych Depression, and three boreholes in the northeastern sector of the Black Sea using lithological, malacofaunistic, and palynological analysis. The Karangatian deposits exposed on the Black Sea shelf contain shells of Didacna cristata and Didacna subcatillus molluscs of Caspian origin. These are characteristic species of the Hyrcanian transgressive basin that developed in the Caspian during MIS 5. Molluscs migrated to the Karangatian Basin through the strait that opened in the Manych Depression. The waters of the strait flowed into the Karangatian Basin in the final phase of its development. During the maximum phase of the Karangatian transgression, its waters penetrated far into the Manych Depression, forming an ingression bay. The flow of the Karangatian waters into the Caspian Sea has yet to be established.