Southern blot analysis of ribosomal DNA (rDNA) from seven species of Apodemus was carried out in order to examine the genetic relationships between the species. Analysis of heterogeneity in rDNA spacers in A. sylvaticus, A. flavicollis, A. semotus, A. agrarius, A. argenteus, A. speciosus, and A. peninsulae, using 13 different restriction enzymes and cloned mouse rDNA probes, revealed that the families of rDNA in these species can be characterized by restriction maps which show the major constituents of rDNA repeating units (repetypes). Based on differences in the arrangement of restriction sites, sequence divergence among the different major repetypes was estimated. Among the seven species of Apodemus examined, the major repetypes of A. flavicollis and A. sylvaticus were the most closely related, having only 1.0% sequence divergence. These repetypes and those of the remaining five species differ substantially from one another, with 4.3-8.5% divergence.