We report sequences of the mitochondrial cytochrome b (1146 bp) and 12S rRNA (961 bp) genes, as well as the nuclear protamine P1 (608 bp) gene, from 13 species representing all four genera of the dasyurid marsupial subfamily Sminthopsinae. Mitochondrial sequences are partitioned into five categories (three codon positions in cytochrome b, and stems and loops in 12S rRNA) with distinct substitution rates, transition biases, and base compositions. We extract estimates of these biases from the sequences and employ them to calculate two overall distances based on the DNAML model. Phylogenetic analyses using distance and parsimony methods yield trees with different topologies for mtDNA and protamine. These trees are compatible with respect to highly resolved nodes, but incompatible with respect to length differences in a parsimony framework. The tree from combined-data analysis is dominated by the larger data set (mtDNA). The balance of evidence favors a basal separation of Planigale from other sminthopsines. Within Planigale, Pl. maculata is sister to the remaining species. Although the precise intergeneric affinities of Antechinomys are unresolved, A. laniger does not appear to be part of the genus Sminthopsis as suggested by morphological data. The 12S rRNA resolves Ningaui ridei and N. yvonnae as sister species.