Sexual dimorphism is a widespread phenomenon throughout the animal kingdom and has attracted considerable interest in evolutionary biology. Studies on sexual dimorphism in hynobiid salamanders, which exhibit external fertilization and have two different habitat preferences, are limited. In this study, we analyzed sexual size and shape dimorphism of the stream-dwelling salamander Batrachuperus pinchonii based on deposited specimens, which were collected from the same locality with the same sampling date, and then explored if either habitat influences sexual dimorphism. Our results revealed no sexual dimorphism in body size (expressed by snout–vent length); however, other morphometric data indicated a female-biased dimorphism in head length, head width, distance of extremities, chest width, and a male-biased dimorphism in foreleg length, foreleg width, fore palm width, hindleg width, and hind palm width. These results would give some merit for future ecological and functional studies on reproduction in B. pinchonii. That is, female-biased head shape is likely related to ecological selection (e.g., reduction of intersexual food competition) and reproductive investment (e.g., intake of more energy). A female-biased trunk dimorphism may contribute to a fecundity advantage (e.g., increase in reproductive output). Male-biased limb dimorphism may relate to reproduction success. We failed to find dimorphic characteristics related to habitats.