To further understand the development process of intermuscular bones in teleosts, a modified bone clearing and staining experiment was conducted to investigate morphological development of intermuscular bone in Japanese eel Anguilla japonica. It is showed that all the axial skeleton and appendicular skeleton both have completely ossified in the glass eel stage. However, the intermuscular bone does not ossify. During the elvers period, the ossification of epineurals, epicentrals and epipleurals is observed in the anterior part of the body. Each of the intermuscular bones is ossified posteriorly, which is very different to that in other species in Cyprinidar. The results indicate that the forming process of intermuscular bones might have relation with the swimming modes. This study provides some very important information about the morphological development of intermuscular bone in Japanese eel, which will be helpful for us to further understand the molecular mechanism underlying intermuscular bone development.