Clarifying the validity of characters that can classify similar rodent species can contribute to defining species quickly and accurately. We identified 36 sympatric rats into R. norvegicus (n = 31) and R. tanezumi (n = 5) by aligning the partial sequence of Vkorc1 gene (725 bp). Based on the identification results of Vkorc1 gene, we compared the accuracy of the classification and identification results of the two species by principal component analysis and cluster analysis of morphology and skull indices, which included 21 permutations of body weight, body length, tail length, ear length and hind foot length, tail length/body length, hind foot length/body length and fatness, and 2 combining indices of skull metrics. The body metrics combination of tail length/body length, ear length/body length, and fatness accurately classified all individuals of the two species. The skull morphology index combination of the length of the upper cheek tooth row, length of the lower cheek tooth row, length of the tympanic bulla, and width of the tympanic bulla also all individuals of the two species. These results provided the critical body or skull morphological characters and corresponding analytical approaches for classifying and identifying the two species.