Before the birth and isolation of the Paratethys by the collision of the Eurasian, Indian, African and Arabian plates, a vast amount of water connected the Central Asian basins, ranging from the Tarim Basin in present day western China to the eastern Mediterranean. This was a large shallow sea referred to as the proto-Paratethys. During the Eocene, the eastern margin of this sea showed a large westward shift, which happened by 5 transgressive and regressive cycles. Recent research in the Tarim Basin has shown that the second-last marine incursion took place during the Bartonian and the last and last marine incursion during the early Priabonian. A logical next step would be to date the retreat of the sea from the Afghan-Tajik Basin, which is situated to the west of the Tarim Basin. This would give a better picture of the extent of this retreat, which would provide more insight in the paleogeography of Central Asia during the late Eocene, and on the shift from this proto-Paratethys to the Paratethys Sea. Also this could shine a light on the possible causes and implications of this sea retreat. This was done in this study by magnetostratigraphic analyses of the continental deposits directly following the last marine sediments at four different locations in the Afghan-Tajik Basin in southwestern Tajikistan. It was chosen to focus the paleomagnetic investigation on the continental deposits as previous studies on similar marine sediments did not give reliable results. Based upon lithostratigraphic correlations of the sections in the Afghan-Tajik Basin with the sections of the Tarim Basin, it was found that the last 2 transgressions found in the Tarim Basin were also present in the Afghan-Tajik Basin. This is a good indication of the retreat from the two basins being part of the same process. Ás the last sea retreat from the Tarim basin was during the early Priabonian, the last retreat from the Afghan-Tajik Basin is also likely to have taken place during the Priabonian. The sampled sections however, which were on top of the last marine sediments have ages of most likely Oligocene age. This suggests that the disconformity found in the Tarim Basin at the Eocene-Oligocene transition (EOT), associated with a major sea level drop, is also present in the Afghan-Tajik Basin. This would then give the last retreat from the Afghan-Tajik Basin a Priabonian age between ~37Ma and ~34Ma, the age of the last retreat from the Tarim Basin and the EOT. There was also looked at the rotations, and it was shown that the sections had undergone a counterclockwise rotation between 20° and 30°. The retreat is likely to be caused by a combination of eustatic sea level changes during the late Eocene, and early uplift processes of the Pamir mountain range as shown by a rotational analysis done in this study. It has been suggested that the presence of the large epicontinental sea in Central Asia was a major contributor to the moisture on the Asian continent. As shown in this thesis, during the final sea retreat the eastern margin of the sea shifted over 500 km to the west, which makes it reasonable to suggest that this has had a great impact on the moisture supply to the Asian continent.