The production of fingerlings on a large scale is one of the biggest challenges for grouper aquaculture development. Groupers may be more susceptible to skeletal anomalies due to their complex skeleton formation ontogenesis. Such anomalies are normally associated with inadequate larviculture protocols for marine fish. The present study aimed to record the occurrence of skeletal anomalies in dusky grouper Epinephelus marginatus. Different degrees of kyphosis, lordosis, and scoliosis were identified. After the larviculture period (60 days), 42% of the dusky grouper presented skeletal anomalies. Therefore, we have concluded that the current protocol for the dusky grouper larviculture must be re-examined, especially to determine a more appropriate water flow in the tanks.