The osteological development of the vertebral column and the caudal complex of the clownfish Amphiprion ocellaris, an important ornamental species is described. The organisms were reared under controlled conditions from hatching until 30 days post hatch (DPH) and methods for the clearing and differential staining of bone and cartilage tissues were applied. At hatching time, most of the vertebral elements had developed in cartilage stage and the notochord in pre-flexion larvae; 11 neural arches were located in the abdominal region while 12 neural arches and 12 haemal arches were found in the caudal region. In the caudal complex, the hypurals were still separated from one another. On 6 DPH the notochord was in flexion stage and the ventral ribs were observed, while 12 neural spines and 12 haemal spines had developed in the caudal region and the hypurals were fused. The notochord was in the post-flexion stage on 11 DPH and the complex caudal completely formed with all the neural spines and haemal spines fully developed. At 23 DPH all structures had ossified. The vertebral column was divided in the abdominal region and comprised of 11 vertebrae while in the caudal region there were 15 vertebrae including the urostyle. Detailed information of osteological structures serve as a reference for the timely detection of malformations during clownfish aquaculture.