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[Display omitted] • The phylogeny of leaf-mining flies is reconstructed using anchored phylogenomics. • A new subfamily clade is proposed, Ophiomyiinae. • Divergence times for leaf-mining fly lineages are inferred from molecular data. Leaf-mining flies (Diptera: Agromyzidae) are a diverse clade of phytophagous Diptera known largely for their economic impact as leaf- or stem-miners on vegetable and ornamental plants. Higher-level phylogenetic relationships of Agromyzidae have remained uncertain because of challenges in sampling of both taxa and characters for morphology and PCR-based Sanger-era molecular systematics. Here, we used hundreds of orthologous single-copy nuclear loci obtained from anchored hybrid enrichment (AHE) to reconstruct phylogenetic relationships among the major lineages of leaf-mining flies. The resulting phylogenetic trees are highly congruent and well-supported, except for a few deep nodes, when using different molecular data types and phylogenetic methods. Based on divergence time dating using a relaxed clock model-based analysis, leaf-mining flies are shown to have diversified in multiple lineages since the early Paleocene, approximately 65 million years ago. Our study not only reveals a revised classification system of leaf-mining flies, but also provides a new phylogenetic framework to understand their macroevolution. [ABSTRACT FROM AUTHOR]