Development of the internal structures of the caudal region (muscles, bones, cartilages, nerves, and blood vessels) of the Da/Da mutant medaka and of wild-type +/+ fish was compared. Muscles and nerves were immunochemically stained by using an antibody to troponin T and antibodies to neurofilament proteins, respectively. Bones and cartilages were stained with alizarin red and alcian blue. In stages 31–32 of the Da/Da embryo, the rudiments of epurals 1, 2, and 3 differentiated dorsally opposite the sites of the ventral rudiments of the parhypural, the lower hypural plate, and the upper hypural plate, respectively. In the +/+ embryo, the rudiments of epurals 1 and 2 differentiated in the later developmental stages (after stage 34), but the rudiment of epural 3 did not differentiate. In the Da/Da embryo, the deep dorsal flexor passed dorsalwards and ended at the rudiment of epural 2, whereas the muscle passed ventralwards and ended at the rudiment of the upper hypural plate in the +/+ embryo. In the Da/Da fry, the epichordal region of the caudal fin fold grew and the notochord extended straight into the tail without bending, while in the + /+ fry, the epichordal region did not grow and the notochord turned dorsalwards within the tail. In the Da/Da fry, extra skeletal rudiments and musculature differentiated in the epichordal region of the caudal fin, whereas these supernumerary structures did not develop in the +/+ fry. The pattern of the epichordal skeleton and musculature in the caudal region of the adult Da/Da fish was an almost mirror-image duplication of the hypochordal structures. These observations suggest that the characteristic expansion of the dorsal fin and epichordal lobe in the caudal region of the adult Da/Da fish is due to a process of ventralization, whereby the dorsal skeleton, musculature, and fin fold are stimulated to differentiate in a pattern like that which is restricted to the anal fin and hypochordal lobe of the wild type.