Résumé
Abstract Whole‐genome sequencing has transformed our capacity to study population structure, define taxonomic boundaries and evaluate evolutionary and conservation processes. By capturing genome‐wide variation, these data provide unparalleled clarity in discerning recent divergence, gene flow and demographic history, even among closely related populations or subspecies. The British swallowtail butterfly ( Papilio machaon britannicus ), a habitat specialist restricted to the fenlands of eastern England, is a compelling example of how genomic data can inform subspecies delimitation and conservation status. Through whole‐genome sequencing of P. machaon populations across Europe, we demonstrate that P. m. britannicus forms a genetically distinct and isolated lineage. In contrast, continental subspecies, such as P. m. gorganus and P. m. machaon , are genomically indistinguishable and should be considered a single, widespread subspecies. Although P. m. britannicus displays ~20% lower heterozygosity than its continental relatives, it retains moderate genetic variation and shows no evidence of an elevated load of deleterious mutations. However, we found significantly higher inbreeding and extended runs of homozygosity, which could raise concerns about its long‐term viability. Demographic modelling based on the site frequency spectrum revealed limited power to resolve recent population size changes; however, weak historical gene flow from the continent was inferred. Overall, our study demonstrates the effectiveness of whole‐genome data in resolving fine‐scale population structure and guiding conservation assessments for range‐restricted taxa.