The purpose of this study was to examine the impact of graded levels of dietary vitamin A on sea bass larval performances and to determine optimal retinol levels at different larval stages to avoid specific skeletal malformations. Retinol was incorporated into larval feeds at 0, 5, 10, 15, 25, 35 and 70 mg kg− 1 dry matter (giving rise to RET0, RET5, RET10, RET15, RET25, RET35, RET70 groups, respectively). Analysis of the several types of deformities affecting the skull, vertebral column or fins of the fish were observed depending on experimental groups. On one hand, the incidence of skull malformations affecting the maxillary and premaxillary bones, dentaries, operculum, branchiostegal rays and glossohyal was lower for the RET0 and RET5 groups. On the other hand, the frequency of vertebral (slight fusions and kyphosis of the anterior five vertebrae, over-mineralization and lordosis of the haemal vertebrae, the transformation of the last pre-haemal vertebra into haemal) and fin (deformations of the dorsal and anal pterygiophores, deviations of the related rays, modifications of the anatomy of the caudal supporting elements, partial to complete lack of the pelvic fins) deformities were lower for the RET5–70 groups. In the RET0 group, lower level of Hoxd-9 expression coincided with partial or complete lack of pelvic fin. Our results suggest that the optimal level of retinol for harmonious ontogenesis fluctuate along sea bass larvae development and that inadequate dietary retinol levels alters morphogenesis through the modulation of Hox gene expression, at least for the pelvic fin.