Over eight kilobases (kb) of sequence from eight genes including two mitochondrial loci, Cytb and 12S, and six nuclear loci, B2m, Zp3, Tcp1, Sry, Smcx and Smcy, were used to investigate phylogenetic relationships among 11 taxa representing eight species within the rodent genus Mus. Particular attention was given to discerning relationships among species within the subgenus Mus including members of a Palearctic clade (M. musculus, M. spicilegus, M. macedonicus and M. spretus) and members of an Asian clade (M. caroli, M. cookii and M. cervicolor), as previous studies using different datasets have produced different topologies for taxa within these two groups. While parsimony analyses of the combined eight-gene dataset yielded a single, fully resolved tree, support values were lower for nodes resolving relationships within the Palearctic and Asian clades than they were elsewhere in the tree. In addition, a maximum likelihood analysis of the same eight-gene dataset yielded different topologies for both the Palearctic and the Asian clades. Both observations are indicative of clade instability. The nature of this instability was explored through a comparison with our previous study in which we included the two mitochondrial loci and only four of the six nuclear genes, and through an analysis of partitioned data, specifically mitochondrial vs. nuclear genes. This study underscores the importance of considering among-site rate variation in phylogeny reconstruction. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 84, 653–662.