Giant Grouper (GG) is a valuable aquaculture species in Southeast Asia. Its farming is challenging, and the occurrence of spinal deformities is one of the bottlenecks found in aquaculture production. This study investigated the development of the swim bladder (SB) in GG and a possible causative relationship between failing to inflate the swim bladder and spinal deviations in juvenile fish. The ontogeny of the swim bladder in GG revealed that the organ is connected through the pneumatic duct to the digestive tube from day 4 to day 7 post hatching (DPH). Repeated observations of larvae over this period showed that GG SB inflation period commences on day 5 DPH and lasted until the end of day 7 DPH. However, a proportion of day 7 DPH larvae failed to inflate their SB showing histological abnormalities in the swim bladder. Later assessment of skeletal anomalies in post metamorphic fish (42 DPH) revealed a relationship between the lack of an inflated swim bladder and anomalies in the caudal region; more specifically, the urostyle (p<0.05). Subsequently, a morphological assessment of juvenile fish showed a direct relationship between the lack of swim bladder and lordotic/kyphotic anomalies. This assessment was confirmed by X-ray of fish with and without a SB following separation by hypersaline flotation. These findings show that failure of larval swim bladder inflation is the major contributing factor to spinal lordotic anomalies in GG. Also, this study described the timing of the swim bladder inflation period in GG and its development.