The chrono-cultural sequence of the Levantine Upper Paleolithic went through several major revisions during approximately a century of focused research, each revision contributing to shedding light on the mosaic of cultural entities and the complex social and cultural dynamics composing the Levantine Upper Paleolithic. The current state of research suggests the co-inhabitance of two cultural groups: the Early Ahmarian and the Levantine Aurignacian. Two other cultural entities, the Arkov-Divshon and the Atlitian, are regarded as younger manifestations and were tentatively suggested to relate to the Levantine Aurignacian. This paper presents a research synthesis of two case studies: Manot Cave, located in western Galilee, Israel, and Nahal Rahaf 2 Rockshelter in the Judean Desert. The application of high-resolution excavation methods, alongside detailed documentation of the stratigraphy and site-formation processes and wide-scale radiocarbon-based absolute dating, marked these sites as ideal for chrono-cultural study through the analyses of flint industries. The results indicate a clear distinction between the Levantine Aurignacian and the Arkov-Divshon/Atlitian industries and a chronological overlap between the Arkov-Divshon, Levantine Aurignacian, and possibly with the Early Ahmarian. Subsequently, we suggest another revision of the currently accepted chrono-cultural model: not two, but at least three cultural entities co-inhabited the Levant at ca. 40–30 ky cal BP. This study further suggests an evolvement of the Atlitian flint industries from the Arkov-Divshon and stresses the foreign cultural features of the Levantine Aurignacian. These results were used to construct an updated model of migration and possible interaction patterns.