This study was carried out to observe the development of the autonomous skeletal development of the Favonigobius gymnauchen. Total length (TL) of larvae 3 days after hatching (DAH) were mean TL of 3.34 mm, with a line-shaped parasphenoid ossification in the cranium and basioccipital ossification in the back. The 10 DAH larvae had a mean TL of 5.20 mm, with the number of caudal vertebrae increasing to 15. The urostyle and two hypural bones in the lower part also began to ossify. The 23 DAH juveniles had a mean TL of 8.47 mm. The pectoral girdle’s skeleton was completed as the scapula and coracoid were ossified. The pelvic girdle also fully supported the ventral fin as its ossification was completed. Favonigobius gymnauchen and Tridentiger obscurus showed similar characteristics in terms of the anus location of hatched larvae, number of myotomes, and melanophore distribution during the morphological development of the larvae and juveniles. However, this study confirmed differences in the development of the vertebrae and urostyle bone.