While the Neogene history of the Eastern Mediterranean region is now fairly well understood, our knowledge of older regional palaeogeographies is less accurate, especially the positions of blocks and nappes constituting the Aegean Islands prior to the Cenozoic. Our study focuses on the ophiolite exposed on the island of Karpathos (Dodecanese), which is located in the Aegean fore-arc at a pivotal position between the ‘western’ and ‘eastern’ ophiolites of the Mediterranean region and where conflicting Late Jurassic and Late Cretaceous ages have led to diverging tectonic and palaeogeographic interpretations. To test these ages, we targeted the radiolarian cherts that depositionally overlie the ophiolite and extracted diagnostic radiolarian assemblages of Aptian (~125−113 Ma), early–middle Albian (~113−105 Ma) and Turonian (~93.9−89.8 Ma) ages. These results suggest that previous Late Cretaceous K–Ar isotopic ages (from 95.3 ± 4.2 Ma to 81.2 ± 1.6 Ma) may have been reset by Late Cretaceous metamorphism or affected by argon loss. Overall, the new Early Cretaceous ages show that the Karpathos ophiolite should not be correlated with the Pindos Nappes of Greece or the ophiolites of Cyprus or Syria but rather with the Lycian Nappes of Turkey and their root located in the Izmir–Ankara–Erzincan Suture Zone. Therefore, the Karpathos ophiolite represents a remnant of the Northern Neotethys, not the Pindos Ocean or the proto-Eastern Mediterranean Basin.