Since European colonisation of Australia, bandicoots in the genus Isoodon have been heavily affected by the introduction of feral predators and changes to the landscape, resulting in the contraction of their distribution and loss of genetic diversity. Their taxonomy has also been a challenge: 11 species were originally described, with revisions in the 1990s leading to recognition of only three species, but recent studies utilising molecular and morphological analyses led to documentation of two additional species. As a result, five species are currently recognised. To further resolve the taxonomy of this genus, we have opted for a total evidence approach, using both morphological and molecular techniques, including sampling specimens from their historical and extant distributions. All available type specimens were also examined and sampled for DNA analyses. Molecular data were generated from 1000s of nuclear gene loci using exon capture as part of the Oz Mammal Genomics initiative. Our results support two additional species (I. microtis, I. moresbyensis new stat.) being raised (recognising seven species in the genus), a major range extension for I. fusciventer and range reduction for the endangered I. obesulus obesulus, and several previously unnamed new subspecies (I. auratus bundilarri, I. a. marchinbarensis, I. fusciventer dawensis, I. f. halae, I. f. insulanus, I. f. terrenus, I. macrourus capensis). This new taxonomic framework has important implications for the conservation management of Isoodon species, with current translocation plans to mix populations, as most species are currently listed as endangered or vulnerable.