Summary Several studies have evaluated the effects of dietary vitamin A (VA) on the incidence of skeletal deformities during early ontogeny of fish, but little is known about its effects on bones depending on their process of ossification (dermal or chondral). We examined the incidence of skeletal deformities along development (30 and 48 dph) by double staining technique, in dermal (haemal and caudal vertebral bodies) and chondral (neural and haemal spines, epural, parahypural and hypurals) bones in Senegal sole post metamorphosed larvae fed with different dietary VA levels (37 000, 44 666, 82 666 and 203 000 UI total VA kg−1 DW) during Artemia feeding phase (6–37 dph, at 18°C). Results obtained in this study showed that dietary VA disrupted the skeletogenesis in Senegalese sole post metamorphosed larvae by increasing the incidence of skeletal deformities in the axial skeleton and caudal fin complex, which were dependent on both bone morphogenesis and ossification processes. Fish fed with the highest dietary VA content showed the highest incidence of skeletal deformities and its value increased along ontogeny. However, when we compared the incidence of deformities in skeletal structures considering their ossification process, most skeletal structures derived from chondral ossification showed a significant higher increase in deformity incidences in fish fed an excess of VA (44 666, 82 666 and 203 000 UI kg−1 DW), however within chondral bones, hypurals deformity incidence only increased in sole larvae fed Artemia highest VA content. In contrast, this dietary dose-response effect was only noted in dermal bones from fish fed the highest dose of VA (203 000 UI kg−1 DW). In addition, the incidence of deformities in chondral bones increased even when the dietary imbalance of VA was corrected, whereas dermal bones were not affected at later ages. These results indicated that depending on the ossification process from which different skeletal structures are derived, bones might be differentially affected by high dietary VA content. Those directly originated from the connective tissue with a preliminary cartilage stage were more sensitive to dietary VA excess than those formed by intramembranous ossification.