The bony labyrinth is often studied in paleoanthropology for the taxonomic identification of hominins with a special focus on the differentiation between Neanderthals and modern humans. Although the variability of Pleistocene populations is now well studied, the variability of Early and Middle Holocene modern human hunter‐gatherers is still poorly known. Thus, this study focuses on the analysis of the bony labyrinth morphology of nine Late Mesolithic individuals from Moita do Sebastião in the Tagus Valley (Portugal). The results show a significant intra‐site variability in the Middle Holocene sample, confirming previous studies on the variability of early modern humans. The analysis also revealed morphological differences in the inner ear structures between European individuals associated with an Upper Paleolithic context (Gravettian) from the Vézère Valley and the Mesolithic individuals from Moita do Sebastião. Interestingly, the only Late Pleistocene individual from Portugal shows some similarities with the Middle Holocene ones, posing the possibility of an eventual local biological continuity.