The mouse 5S rRNA gene was mapped by direct R-banding fluorescence in situ hybridization (FISH) with biotinylated probes. Two genomic fragments amplified by PCR from total genomic DNA of BALB/c mice and Mus spretus, a 0.16-kb fragment that included the 121-bp 5S rRNA gene and a 1.6-kb fragment that included the whole spacer region, were used for chromosomal mapping of the 5S rRNA gene. Both fragments hybridized to a single locus on a pair of autosomal chromosomes of BALB/c mice. The major cluster of mouse 5S rRNA genes was assigned to the most terminal R-negative to R-positive bands of the E region of mouse Chromosome 8, which is homologous to the linkage of the 5S rRNA gene on the long arm of human chromosome 1. The location of the 5S rRNA gene was mapped in five laboratory strains, in wild mice of six Mus musculus subspecies (domesticus, brevirostris, musculus, bactrianus, castaneus, and molossinus) derived from 10 separate localities, and in four different Mus species (spretus, hortulanus, spicilegus, and caroli), using FISH. The 5S rRNA cluster mapped to the same position on the chromosomes of all mouse species and subspecies studied. These results suggest that the location of the mouse 5S rRNA gene on the distal telomeric region of Chromosome 8 is evolutionarily conserved. In comparison, the chromosomal assignments of centromeric 18S-28S rRNA genes are highly variable among the different M. musculus subspecies and Mus species.