The Cansona and San Cayetano formations are the oldest sedimentary units of northwestern Colombia and record the beginning of the convergence between the proto-Caribbean and South American plates. Previous micropaleontological studies on these units indicate the presence of planktonic foraminifera, calcareous nannofossils, and pollen, with limited biostratigraphic resolution. This study challenges this issue by reporting for the first time a late Cretaceous and early Paleocene radiolarian inventory from several silicified siltstones and cherts of the Cansona and San Cayetano formations. Although radiolarian occurrences are rare, we report 21 species that characterize the Late Cretaceous radiolarian assembly and belong to the genera Alievium, Amphipyndax, Archaeodictyomitra, Archaeospongoprunum, Calocyclas, Cornutella, Dictyomitra, Dictyoprora, Foremanina, Mita, Pseudoaulophacus, Pseudotheocampe, Siphocampe, Stichomitra, Theocapsomma, Criptamphorella, Crucella, Patellula, and Triactoma. Equally rare occurrences of radiolarians are found in the Paleocene, were Early Paleocene-restricted Amphisphaera aotea Hollis, together with other spumellarians, notably Amphisphaera cf. A. kina Hollis, Artostrobus pusillum (Ehrenberg), Lithostrobus longus Grigorjeva and the nassellarian Buryella granulata (Petrushevskaya) considerably shortened the Cretaceous-Paleogene boundary hiatus. The present work concludes that the Late Cretaceous radiolarian dating reinforces the present state of knowledge on the Cansona Formation and reveals new biostratigraphic evidence regarding the presence of earliest Paleocene sequences in the San Cayetano Formation. This is an important result for understanding the geological evolution of the Cretaceous proto-Caribbean margin.