Two morphotypes, with a large and small body size, of a brown frog Rana t. tagoi occur sympatrically in the Kinki region, central Honshu of Japan. Previous mitochondrial (mt) DNA genealogical study recognized two main lineages (A and B) and several sublineages in R. tagoi, where the small type was placed in the group A-1b, and the large type in groups A-1a and B-2a. Using haplotype network and structure analysis of three nuclear genes, we examined the discrepancy between morphology and mitochondrial genealogy. The results showed that the small type is reproductively isolated from its co-occurring large type (A-1a or B-2a), and that unlimited gene flow occurred between parapatrically occurring two mtDNA lineages of large types (A-1a and B-2a). Discordant genetic relationships between mtDNA and nuclear DNA results may be caused by the past mitochondrial introgression, and possibly, the incomplete lineage sorting. These results also suggest a heterospecific relationship between the large (A-1a and B-2a) and small types (A-1b). The large type is identified as Rana t. tagoi as it is genetically very close to the topotypes of the nominal subspecies, while the small type remains unnamed.