The hynobiid salamander genus Hynobius is a basal taxon in the urodeles that plays a key role in understanding the evolution of sexual dimorphism in urodeles. We examined the age (juveniles vs. adults) and sexual differences in the external and skeletal morphology of a Japanese lentic breeding salamander, Hynobius setouchi. We found that juveniles had larger heads than those of adults, and most characters were larger in adult males than in females, except for trunk size. This was also observed in skeletal morphology, although some tail characters differed only in the skeleton. We suggest that intra- and interspecific comparisons of the external and skeletal characters of salamanders should consider age, sexual, and seasonal differences.