Drosera (Droseraceae) is one of the largest carnivorous plant genera globally, with Australia considered a nexus for the evolution of the genus. We present the most densely sampled phylogenomic analyses for Australian Drosera to date. As part of the Genomics for Australian Plants Initiative Stage II, 92 Drosera samples representing all major clades within Australia and key extra-Australian taxa were newly sequenced using Angiosperm353 and OzBaits nuclear bait sets, and the OzBaits plastid bait set. In total, 380 nuclear and 57 plastid loci were included in our final analyses. Our findings are broadly in congruence with conclusions of previous morphological studies that were informed by molecular data regarding the major lineages within Drosera. Incongruencies between the results from plastid and nuclear sequence data sets were primarily restricted to within-clade relationships, with high discordance noted in two closely affiliated species groups with centres of diversity across northern Australia and south-west Western Australia. Potential drivers of this phylogenetic discordance are investigated using Quartet Sampling and are discussed. An important outcome of these data is to highlight the diversity of novel evolutionary lineages within Australia for this group of plants that exhibit highly modified traits to survive in arid Australian environments.