This doctoral thesis is presented in three chapters. The first chapter is a phylogenetic analysis of the lower Cyclorrhaphan (Insecta: Diptera) families of Diptera. These families form a non-monophyletic grade, and have been a long-standing problematic section of the Dipteran tree of life. We attempted to bring resolution to this assemblage of families using a combination of transcriptomic and anchored hybrid enrichment data from 43 ingroup taxa. Results were largely concordant with existing molecular phylogenetic efforts, but Lonchopteridae remains problematic to place. The second chapter of the thesis is a more detailed phylogenetic analysis of a single lower Cyclorrhaphan family, the Syrphidae. This chapter has also been published as an open-access paper in BMC Evolutionary Biology. Subfamilial boundaries within Syrphidae are a known problem, and there has been little consensus on how to treat the paraphyletic subfamily Eristalinae. We used a novel anchored hybrid enrichment probe kit to produce a 30 species phylogeny of Syrphidae with strong support values across the entire tree. As expected, a paraphyletic Eristalinae was recovered. Our sampling was not rigorous enough to produce a stable revised classification, but we hope this chapter will act as a starting point for a future overhaul of the subfamily. This chapter has been published as an open-access paper in BMC Evolutionary Biology. The final chapter of the thesis was also Syrphidae-focused, with a taxonomic revision of the Australian Psilota. The revision is based on a combination of Cytochrome c Oxidase I DNA barcodes and morphological analysis. The number of known Australian Psilota species was increased from 16 to 30, with two acknowledged species complexes that should be revisited in the future. All species are fully described and illustrated, with external habitus and male genitalia photographs.