This study focused on the anatomy and ontogeny of saddleback syndrome (SBS) in reared European sea bass. The abnormality was detected at an unusually high frequency (12–94%) during a routine quality control in a commercial hatchery. Anatomically the abnormality was mainly characterized by the loss of 1–5 hard spines and severe abnormalities of the proximal pterygiophores (anterior dorsal fin), size reduction of a few lepidotrichia, missing lepidotrichia and/or lepidotrichia of poor ossification (posterior dorsal fin). SBS was significantly correlated with abnormalities of the anal and pelvic fins in all the examined populations. Moreover, in juvenile fish, SBS was significantly correlated with an abnormal lack of sectors of the lateral line. The examination of early larval samples revealed that SBS was ontogenetically associated with severe abnormalities of the primordial marginal finfold, which developed at the flexion stage (ca 8.5–11.0 mm SL). Histologically, these abnormalities were associated with extensive epidermal erosion. The results are discussed in respect of the critical ontogenetic period and the possible causative factors of SBS in European sea bass. It is suggested that causative factors acted during a wide ontogenetic period including flexion and metamorphosis phases.