The Anthomyiidae have been recovered as paraphyletic with regard to the Scathophagidae in several recent molecular analyses and need resolution. We address this issue by producing a robust phylogeny of the family Anthomyiidae, based on a broad sampling of anthomyiid genera and over 300 single-copy orthologous loci captured using anchored hybrid enrichment (AHE). Most notably, the phylogenomic analyses provide strong support that family rank for Scathophagidae renders Anthomyiidae paraphyletic. We propose a revised classification with a basal Coenosopsiinae Bailey & Michelsen (subfam. nov.), including the Neotropical Phaonantho Albuquerque and the Neotropical and southern Nearctic Coenosopsia Malloch, which emerge as sister taxa and together comprise one of the two earliest diverging clades; a Hyporitinae (stat. rev.) including Hyporites Pokorny and the predatory genus Alliopsis Schnabl & Dziedzicki; and a Scathophaginae (stat. rev.) relegated to subfamily rank within Anthomyiidae which includes the former subfamilies Scathophaginae and Delininae as tribes Scathophagini (stat. rev.) and Delinini (stat. rev.).