The gene expressions of BMP1, 2, 4, 5, 7, 10, IGF1 and 2 were detected and quantified in Trachinotus ovatus larvae from 0 day post hatching (DPH) to 18 DPH. The expression of BMPs and IGFs was detected and quantified on 0 DPH at low levels. At first feeding, the expression of BMP1, 2, 4, 5 and 10 sharply increased and reached the peak levels on 3 DPH, while the expression of BMP7 reached the peak level on 5 DPH. On 18 DPH, the expression levels of BMP4 and BMP5 were similar to the levels of fish larvae at hatching, while the expression levels of BMP1, 2, 7, and 10 remained at higher level than their hatching expression levels. Starting from 0 DPH, the expression level of IGF1 increased with the increasing of fish age. In contrast, the expression level of IGF2 reached peak on 3 DPH, and then decreased. Results of the present study provide the first reference on the BMPs and IGFs expressions of golden pompano larvae during the ontogenetic development. Such information can improve our understanding on the bone formation in golden pompano, and provide background knowledge to the study of skeleton malformation in fish larvae.