Phylogenetic relationships among the 6 species of quolls (Dasyurus) are resolved using DNA sequences from 4 mitochondrial and 5 nuclear loci (approximately 15 kb) sampled from 1 to 29 individuals per species. Our estimate of quoll phylogeny concurs with previous DNA-based estimates in placing Dasyurus hallucatus as sister to the remaining species, and D. maculatus as sister to a clade containing D. viverrinus, D. albopunctatus, D. geoffroii D. spartacus. We also provide the first formal description of penis anatomy in the northern quoll (D. hallucatus), documenting it as the only species of Dasyurus lacking an appendage to the penis. This appendage thus appears to constitute a morphological synapomorphy for the clade of 5 species that excludes D. hallucatus. The sequence from our single specimen of bronze quoll (D. spartacus) nested within a clade of 3 western quoll (D. geoffroii) sequences, suggesting that the species boundary between these groups (if it exists) is not yet reflected in reciprocal monophyly of mitochondrial haplotypes. Any genetic differences found between eastern and western forms of D. geoffroii would have implications for translocations of western animals into other parts of the species range.