New exposures of marine Miocene deposits in the area of Nowy Targ, have recently been discovered. Four new lithostratigraphic units, being younger than both the Magura and Malcov Beds of the Magura Series, have been distinguished there. The lowermost flysch unit is Oligocene–Lower Miocene in age, whilst the overlying flysch and two molassic units represent the Middle Miocene. Their age is documented by assemblages of foraminifers, calcareous nannoplankton and radiolarians. Steeply dipping, marine Miocene beds display tectonic contact with the Pieniny Klippen Belt. The sediments discussed were deposited in a piggy-back basin formed in the southern part of the Magura Basin. Subsequent folding of the Magura Nappe and intensified thrusting at the Badenian/Sarmatian boundary or later led to regression of the Miocene sea and closing of the basin. At the same time, the last tectonic stage, forming the structual contact between the Pieniny Klippen Belt and the Magura Nappe took place. The origin of the Orava-Nowy Targ intramontane basin, controlled by the beginning of freshwater Neogene sedimentation in it, had to take place in, or after the late Middle Miocene.