The Miltogramminae (Diptera: Sarcophagidae) includes ~600 species across >40 genera, which constitute ~20% of global Sarcophagidae. While molecular phylogenetic hypotheses have been produced for this group, critical problems persist, including the presence of paraphyletic genera, uncertain relationships between genera, a bias of sampling towards Palaearctic taxa, and low support for many branches. The present study remedies these issues through the application of Anchored Hybrid Enrichment (AHE) to a sample including ~60% of the currently recognised genera (16% of known species) representing all biogeographic regions except the Neotropical. An alignment of 1,281 concatenated loci was analysed with maximum likelihood (RAxML, IQ-TREE), Bayesian inference (ExaBayes) and coalescent-based approaches (ASTRAL, SVDquartets), which resulted in highly supported and concordant topologies, providing unprecedented insight into the relationships of this subfamily of flesh flies, allowing a major update to miltogrammine classification. The AHE phylogenetic hypothesis supports the monophyly of a large proportion of genera. The monophyly of Metopia Meigen is restored by synonymy with Aenigmetopia Malloch, syn.n. To achieve monophyly of Miltogramma Meigen, eight species are transferred from Pterella Robineau-Desvoidy. The genus Pterella is shown to be paraphyletic in its current circumscription, and to restore generic monophyly Pterella is restricted to contain only Pt. grisea (Meigen). Erioprocta Enderlein, stat.rev., is resurrected. The genus Senotainia Macquart is reconstructed as paraphyletic. The monotypic genus Metopodia Brauer & Bergenstamm is synonymised with Taxigramma Macquart, syn.n. In light of our phylogenetic hypotheses, a new Miltogramminae tribal classification is proposed, composed of six tribes.