Rhytiphora Audinet-Serville, 1835 is the most speciose longhorn beetle (Cerambycidae Latreille, 1802) genus in Australia, with ~200 species (from nearly 40 former genera, now synonymised into one) distributed across the entire continent. We used mitochondrial genome data from whole genome shotgun sequencing and COI barcoding of museum specimens to reconstruct the phylogeny of 68 Rhytiphora species, and analysed the morphological diversity and biogeographic history. We recovered a monophyletic Rhytiphora containing two distinct clades, within which all of the former genera (except Achriotypa Pascoe, 1875) are paraphyletic. Nine morphological traits (including body size and the male setose ‘sex patches’) show strong phylogenetic signal and can be used to differentiate between the two clades. One clade is mainly restricted to Australia’s tropical north, whereas the other, larger clade has many species along the mesic east coast. Both clades have experienced multiple biome shifts, displaying a remarkable flexibility in habitat occupancy.