Considerable intraspecific variation has been known in the shell morphology of the freshwater snail genus Semisulcospira. However, sexual dimorphism and allometric growth have not been elucidated in the genus, although these factors contribute to generating intraspecific variation. We used a combination of geometric and traditional morphometrics methods (GMM and TMM) in a single population of Semisulcospira niponica to assess sex-related differences in shell size and shape at maturity. The results of a generalized Procrustes analysis of variance revealed significant differences in shell size and shape between males and females. A principal component analysis (PCA) showed allometric differences between males and females; Principal component (PC) 1 values and their overlap between the sexes decreased with size. PC1 explained 35.5% of the total variance, which corresponded to vertical elongation of the shell spire and aperture, and broadening of the shell. The results of a canonical variate analysis using the ten largest specimens of each sex showed that females have less elongate shells with rounder apertures and a broader body and penultimate whorls than males. TMM using nine morphological characters supported shell morphological differences between the sexes and correlations between shell size and shape associated with different growth stages. However, GMM was more sensitive for detecting shape differences than TMM. For example, TMM explained the observed increase in shell diameter primarily as a function of size, whereas GMM detected sex-related differences in shell diameter as shape differences between the sexes. Furthermore, dimorphism and allometry in shell sculpture traits could be explored only by TMM. For accurate evaluation of shell morphology in Semisulcospira, it is important to use larger specimens after separating males and females since the present results revealed intersex differences in size and shape, some of which become more evident with age. It is also essential to employ both GMM and TMM because the two methods capture different aspects of morphological variation in shell outline and sculpture.