Cretaceous pelagic deposits in the Bangong-Nujiang Suture Zone are significant for understanding the last evolutionary stage of the Mesotethyan Ocean and constraining the timing of initial Lhasa-Qiangtang collision, however few existing studies present the necessary sedimentological and biostratigraphic data. Here, we present detailed lithostratigraphic and biostratigraphic surveys in the Rotug area. A total of 40 species belonging to 23 genera are identified in the pelagic siliceous sedimentary sequences and indicate an Early Cretaceous (Hauterivian–late Aptian) age based by correlation on Unitary Association Zones. These newly discovered radiolarians help to constrain the paleoceanography and paleogeography of the Mesotethyan Ocean and indicate a deep marine setting existed across western Tibet during the late Aptian. Faunal similarities across the entire Tethyan realm, suggest this ocean was connected with the Neotethyan Ocean during the Early Cretaceous. This study has implications for the paleoceanographic evolution of the post-collisional residual-sea and sedimentary characteristics of marginal basins adjacent to continents during the Late Mesozoic.