This doctoral thesis is presented in six chapters and aims: (1) to produce the first ever phylogeny of Syrphidae: Eristalinae: Milesiini: Criorhinina using molecular characters and to test current generic concepts; (2) to explore the question of paraphyly within the subfamily Eristalinae; (3) to provide a new framework of tribal and subtribal relationships; (4) to use our phylogeny of Criorhinina to revise generic concepts to which we can assign newly described species. Chapter one presents a phylogenetic hypothesis of the subfamily Eristalinae with an emphasis on the subtribe Criorhinina using eight different molecular markers. Eristalinae was recovered as paraphyletic with strong support for the elevation of Cerioidini, Merodontini and Volucellini to subfamilial status. Criorhinina is restricted to contain Criorhina Meigen, Matsumyia Shiraki, Romaleosyrphus Bigot and Sphecomyia Latreille. Chapters two, three, and four represent revisions of genera or regional revisions of the subtribe Criorhinina. Chapter two revises the 16 world species of Sphecomyia with the description of seven previously undescribed species. Chapter three reviews the genus Romaleosyrphus and includes seven newly described species in the concept. Chapter four reviews the species of Nearctic Criorhina, including the description of three previously undescribed species. Additionally, the sixteen species of Sphecomyia are combined with Criorhina. iii Chapter five presents a targeted enrichment sequencing phylogeny to reveal a new hypothesis of Eristalinae relationships. Eristalinae is revealed as a paraphyletic assemblage of four monophyletic clades: Eristalinae, Cerioidini, Merodontini, and Volucellini. Multiple independent Australian-Chilean relationships are revealed, raising the question of whether Syrphidae underwent Trans-Antarctic dispersal or Gondwanan vicariance. The final chapter presents SAPPHYRE, an all-in-one dataset preparation software package that bridges the gap between sequencing and analysis. It eschews traditional assemblers in favor of mapping reads directly against reference amino acid translations. Using data from Dietz et al. 2023 we compare the output of SAPPHYRE against PHYLUCE, HybPiper, Orthograph, BWA mapping, IBA, and the combined approaches of Orthograph + Phyluce and Orthograph + Phyluce + Trinity.