Fluorescence in-situ hybridization was used to construct a comparative chromosome map between the laboratory mouse, Mus musculus and the African four-striped mouse, Rhabdomys pumilio. A high degree of homology between the species was detected using both FISH and G-banding. Ten mouse chromosomes (2-4, 7, 14-16, 18, 19 and the X) were retained as chromosomal arms or intact chromosome blocks. Six mouse chromosome painting probes that correspond to mouse autosomes 5, 6, 8, 11, 12 and 13, produced double signals; the remaining four painting probes (1, 9, 10 and 17) hybridized to three or more R. pumilio chromosomes respectively. In total, the 20 mouse chromosome paints revealed 40 segments of conserved synteny in the R. pumilio genome. Most of the mouse chromosomes that produced single signals in R. pumilio have previously been shown to be conserved in the Black and Norwegian rats and the Chinese hamster. Eight contiguous segment associations appear to be R. pumilio specific, two were shared by R. pumilio and the Black and Norwegian rats, but to the exclusion of the Chinese hamster. Our data suggest that mouse chromosomes 1, 10, and 17 have undergone extensive rearrangements during genome evolution in the murids and may be useful markers for enhancing our understanding of the mode and tempo of chromosome evolution in rodents.