A large number of sites dated to the Late Middle Paleolithic and the Early Upper Paleolithic have been recorded in the Cantabrian region (northern Iberia), making this area a key location to investigate the lifeways of the last Neanderthals and the first anatomically modern humans. The stratigraphic sequence from El Cuco rock-shelter was originally attributed to the Early Upper Paleolithic based on radiocarbon dates measured on bone apatite. However, new radiocarbon dates on shell carbonates from the lower levels produced inconsistent dates with those previously published. In order to clarify this anomaly, a reassessment of the chronology of levels VI to XIV was undertaken. The review was based on new radiocarbon dates performed on bones and shells, and a re-evaluation of the lithic assemblages. Bone samples did not produce radiocarbon dates due to a lack of collagen preservation but radiocarbon dating of shell carbonates provided dates ranging from 42.3 to 46.4 ka BP. These dates are significantly older than that previously obtained for level XIII using biogenic apatite from bones (∼30 ka uncal BP), suggesting that the bone apatite used for radiocarbon dating was rejuvenated due to contamination with secondary carbonate. Lithic assemblages, defined in the first place as Evolved Aurignacian, have now been confidently attributed to the Mousterian techno-complex. These results suggest a Middle Paleolithic chronology for this part of the sequence. The new chronology proposed for El Cuco rock-shelter has significant implications for the interpretation of Neanderthal subsistence strategies and settlement patterns, especially for coastal settlement and use of marine resources, not only in northern Iberia, but also in Atlantic Europe.