Skeletal deformities are significant problems that affect the growth and commercial value of fish reared in hatcheries. However, studies of bone metabolic process related to skeletal deformities are limited. We investigated the potential correlation between bone deformities and plasma calcium, phosphorus, and estradiol-17β levels in reared red spotted grouper (Epinephelus akaara) juveniles. We collected E. akaara frys from private farms at 110, 140, 180 and 300 days after hatching (DAH), and classified the normal and deformed fish by observing their external shape and inner frame by soft X-ray. We also analyzed the calcium, phosphorous, and estradiol-17β levels in their plasma. A comparison between normal and deformed fish, indicated that calcium and estradiol-17β levels were higher in deformed fish than in the normal at 180 and 300 DAH. The level of phosphorus was also higher in deformed individuals than in normal fish, but only at 300 DAH. These results suggest that skeletal deformities are associated with increases in plasma calcium, phosphorus, and estradiol-17β levels.