Although the Transylvanian Basin is often referred as part of the Miocene Pannonian Basin System, we point out important tectonic and sedimentary differences reflected in the stratigraphy. The Neogene of the Transylvanian Basin can be split into two tectonic megasequences: Lower Miocene and Middle to Upper Miocene. The Early Miocene onset of the back arc extension in the Pannonian Basin was not observed in the Transylvanian Basin, where shallow to deep marine sediments were deposited in a flexural basin. Diverse types of facies developed in the continental (e.g., Sânmihai) and marine (e.g., Coruş, Chechiş, Hida) Lower Miocene formations. Although these are poorly constrained to the standard biostratigraphy, recent 87 Sr- 86 Sr data support their limited correlation with the Burdigalian. The Middle Miocene extension in the Transylvanian Basin is very weak compared to that the Pannonian Basin. As the high-resolution Middle Miocene regional biostratigraphy of the Badenian and Sarmatian was calibrated by magnetostratigraphy and radiometric dating of the volcanic tuffs up to the Serravallian/Tortonian boundary, the influence of the regional tectonics on the basin's evolution and stratigraphy can be better understood. The regional tectonics produced a progressive basin isolation starting with the late part of the Middle Miocene. The uplift of the Carpathians isolated the basin at the beginning of the Pannonian and initiated the fan delta, lacustrine, and fluvial sedimentation. The basin was rapidly uplifted and eroded, while post-extensional subsidence was still ongoing in the Pannonian Basin. Endemic fossil assemblages allow only regional-scale correlations for this interval. The uppermost part of the stratigraphic record is represented by the volcano-sedimentary formations generated by the late evolution of the Eastern Carpathians. The sedimentation and subsidence pattern of the Transylvanian Basin reflect the effect of retreating subduction zone in the Eastern Carpathians.