The Microtus (Terricola) savii s. l. complex is a group of five species/subspecies of the Italian pine voles, which diverged at different times either with or without chromosomal differentiation. The evidence of chromosomal diversification has so far concerned the shape of the sex chromosomes, especially the X chromosome. Three taxa of the group, M. savii savii, M. s. nebrodensis, and M. s. tolfetanus have identical karyotypes with metacentric X chromosomes. The X chromosomes of M. brachycercus and M. b. niethammericus are, respectively, subtelocentric and acrocentric in shape. The M. savii complex has been long an object of conventional karyological studies, but comparative molecular cytogenetic data were completely missing. Therefore, we conducted a comparative chromosomal mapping of rRNA genes (rDNA) and telomeric repeats in three of the five taxa of the group: Microtus s. savii, M. s. nebrodensis, and M. b. niethammericus, each of which belongs to a distinct mitochondrial clade. The survey revealed that differentiation of the clades was accompanied by remarkable changes with regard to the number and locations of the rDNA sites. Thus, M. s. savii and M. s. nebrodensis have especially high numbers of rDNA sites, which are located in the centromeric regions of, correspondingly, 18 and 13 chromosome pairs, whereas M. b. niethammericus shows variable (8–10) and heteromorphic rDNA sites on both centromeric and telomeric regions. Interstitial telomeric sites (ITS), which are believed to indicate possible breakpoints of recurring chromosomal rearrangements, are present on the largest biarmed chromosomes and on the metacentric X chromosomes in M. s. savii and M. s. nebrodensis. These preliminary results are discussed in the context of recent advances in phylogeny of the group, as well as the rDNA genomic organization and X chromosome rearrangements in the genus Microtus.