Salmincola markewitschi Shedko et Shedko, 2002 (Copepoda: Lernaeopodidae) is an ectoparasitic copepod mainly infecting the buccal cavities of white-spotted charr Salvelinus leucomaenis (Pallas) (Salmonidae). This species has only been recorded from Northeast Asia, where a morphologically similar congener Salmincola carpionis (Krøyer, 1837) is also distributed, using the same host species. These copepods are hard to distinguish from each other because of their similarities. We thus examined the newly collected specimens morphologically and genetically from five populations of white-spotted charr in Japan. Most of the specimens were morphologically consistent with S. markewitschi but showed great variations in the numbers of spines on the exopods of the antennae, shape of the maxilliped myxal palps, and the bulla diameter. Consequently, some specimens shared characteristics with S. carpionis. In addition to the mophological continuities, genetic analyses of 28S rDNA and COI mitochondrial DNA confirmed that all specimens belong to a single species. Further taxonomic revisions are required to draw conclusions of whether S. markewitschi is a valid species different from S. carpionis, by collecting samples from across their wide distributional ranges, such as Europe, North America, and Northeast Asia. A key to identification of species of Salmincola Wilson, 1915 occurring in Japan is also provided.