The genus Mus encompasses 38 species of mice divided into four subgenera: Mus, Pyromys, Nannomys and Coelomys. Each of these four taxa is characterized by discrete morphological as well as biochemical traits. We used two different molecular approaches to determine the relationships between these subgenera: DNA/DNA hybridization and 12S rRNA mitochondrial sequences. We compared the resulting phylogenies from each method and with phylogenies derived from morphological data. The degree of resolution of each molecular approach is discussed. The two molecular studies indicate that Mus, Pyromys, Nannomys and Coelomys are clearly distinct monophyletic groups, as previously indicated by morphological data and other biochemical and molecular approaches. There is one divergence between previous morphological and the molecular and morphological studies presented here: the position of the Indian species Mus famulus. This taxon, which was formerly included in the subgenus Coelomys, is demonstrated here to belong to the subgenus Mus. We also propose the following relationships within Mus sensu lato: Mus and Pyromys are the closest relatives, followed by Nannomys and Coelomys, whose relationships are still unclear. This arrangement is more robustly supported by DNA/DNA hybridization than by 12S rRNA data. A molecular time scale for the evolution within Mus sensu lato is proposed, using as a reference the Mus/Rattus divergence estimated by the fossil record at around 12 mya. © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 137, 385–401.