We analyzed partial sequences (approx. 630 bp) of the 18S nuclear ribosomal RNA gene (rDNA) in the Japanese Eothenomys voles, E. andersoni and E. smithii, to evaluate their evolutionary complexity. There were two rDNA types of sequences with a few substitutions and an indel, and both species alternatively carried one of the two rDNA types, irrespective of their classifications. One of the rDNA types was mainly distributed in Eastern Japan, and the other in Western Japan. Such rDNA type distributions were not related to the species classifications. The complex genomic elements across both species were confirmed by previous studies of nuclear, mitochondrial, and Y chromosomal genes, and our current data agree with previous findings. Previous studies indicated that the genome constitutions of the Japanese Eothenomys species may have been caused by interspecific genetic exchanges at an early period after the speciation into E. andersoni and E. smithii from their common ancestor, as neither species crosses at present. In addition, the present results also suggest the additional hypothesis that their common ancestor might have two (or more) rDNA gene types, and that one of the rDNA types was fixed in each population of both species during their colonization processes.