The alcian blue-alizarin red technique was successfully adjusted to stain developing European sea bass (Dicentrarchus labrax) larvae. For an optimal staining protocol design both larval size and their morphological characteristics at each developmental stage were considered, since such parameters notably influence the staining of tissues. The incubation times of the different solutions were adjusted to allow the stain penetration for revealing the integrity of cartilaginous and bony tissues without significant tissue degradation. Three developmental windows were determined for an optimal staining procedure: (i) 4.5–6.4 mm, (ii) 6.7–8.7 mm, and (iii) 12.8–15.5 mm total length (TL). In order to validate the continuity of staining along the larval development, quantification of bone mineralization and osteocalcin gene expression were also monitored. Quantitative analysis revealed that ossification followed an exponential kinetic that was positively correlated with the osteocalcin gene expression pattern (Rs = 0.9762, P < 0.05). The mineralized tissue increased from 6.4 mm TL onwards, corresponding with the detection of the first ossified structures. The quantity of bony tissue increased gradually until 7.6 mm TL, since mineralization remained limited to the skull. From 8.3 to 15.5 mm TL, the mineralized bone was notable and nearly concerned the whole larval skeleton (skull, vertebral column and caudal complex). Since it was possible to detect the first cartilaginous and mineralized structures in specimens as small as 4.5 and 6.4 mm TL, respectively, this procedure is a useful tool to study the European sea bass skeletal ontogenesis, to precociously diagnose skeletal malformations in small larvae and eventually to better characterize the effect of different environmental and/or nutritional factors on the ossification status of specific skeletal components.