Target capture efficiently resolves the long‐standing taxonomic dead end of <i>Diachrysia</i> moths

Abstract Accurate species delimitation and identification are crucial for assessing biodiversity and conserving species. The Diachrysia cryptic moth complex, comprising D. chrysitis and D. stenochrysis , exhibits overlapping morphological traits, complicating species identification and rendering their status as distinct species debatable. We applied a target enrichment approach leveraging 1753 nuclear single‐copy orthologs to clarify their relationships and test the power of this method in addressing complex taxonomic questions. Phylogenetic and population structure analyses revealed clear nuclear differentiation between the two taxa, contrasting with the variability in wing pattern observed within each species. We also detected rare cases where the mitochondrial DNA barcode region (COI) is shared between the species. This discordance between genetic and morphological variation suggests that wing pattern alone is often unreliable for species diagnosis. Our study advances understanding of the evolutionary and speciation history of Diachrysia and provides an efficient genomic model for addressing complex taxonomic questions of recently diverged sibling taxa.