The otoliths of wild common sole, Solea solea, and Senegal sole, Solea senegalensis, from the Tagus and the Douro estuaries, and captive S. senegalensis were examined for the detection of anomalies. The anomalies detected were granules of crystals, a dark coloration over the entire otolith, a dark mark concentric to the nucleus and multiple nuclei. A higher proportion of anomalies was found in wild individuals of these species (16–63%) than is usually reported for other species. Captive S. senegalensis exhibited an incidence of anomalies within the range previously reported for other species also reared in captivity. The oceanographic–climatic conditions of the Portuguese coast, which cause strong and abrupt changes in water temperature, salinity and mineral composition, may be an important factor contributing to or causing otolith anomalies. Heatwaves, intense solar radiation and anthropogenic pollution affecting the estuarine nursery grounds may also play an important role. However, more experimental studies are needed to elucidate what causes otolith anomalies.