The lack of a robust phylogenetic backbone has posed significant challenges to proposing an infrageneric taxonomic classification of the pear genus, Pyrus, a widely distributed Eurasian lineage of Rosaceae. This issue has been exacerbated by limited informative lociinaccessible taxon sampling. To address these limitations, we conducted extensive taxon sampling, encompassing 78 Pyrus ingroup individuals representing 32 species, along with 4 outgroup species. This comprehensive sampling strategy covers a wide range of morphologicalgeographical variations. To enable accurate phylogenomic inference, we assembled 801 single‐copy nuclear genes72 plastid coding sequences from deep genome skimming (DGS) data. Additionally, we employed a tree‐based method for nuclear orthology inference, which led to the generation of three orthologous datasets: one‐to‐one orthologs (1to1), monophyletic outgroups (MO),rooted ingroups (RT). The results yielded from both nuclearplastid analyses consistently support the monophyly of Pyrus,two well‐supported clades, the OccidentalOriental clades, were recovered in nine nuclearthree plastid trees. Integrating evidence from morphologyphylogenomics, we propose an updated infrageneric classification of Pyrus, which consists of two subgenera: P. subg. PyrusP. subg. Pashia stat. nov. This revised classification provides a more robust framework for understanding the evolutionary relationships within the pear genus.