A cryptic loach species of the genus Misgurnus (Cypriniformes: Cobitidae) has been reported as Misgurnus sp. Type I sensu Okada et al. (2017) (hereafter called Type I loach) from the Japanese Archipelago, in addition to the common nominal species, M. anguillicaudatus (hereafter called Type II loach). Although both species co-exist in the Naka-ikemi Wetland, Fukui Prefecture, their mechanism of reproductive isolation is unknown. Differences in sexual dimorphism might reflect differences in reproductive behaviour that contribute to reproductive isolation between the two species. We investigated the morphological characteristics of the two loach species at two sympatric sites and observed several morphological differences. Type I differ from Type II loaches in the following morphological traits and sexual dimorphisms: in males, generally less developed lamina circularis, shorter anal fins, and lack of a pair of raised ridges in the anterior portion of the body side; in females, lack of spawning scars on the body side. These morphological differences between the two sympatric loaches may reflect differences in their spawning behaviour. Furthermore, it may represent one of the factors responsible for reproductive isolation between the two species.