This study addresses the longstanding absence of a comprehensive phylogenetic backbone for the apple tribe Maleae, a deficiency attributed to limited taxonmarker sampling. We conducted an extensive taxon sampling, incorporating 563 plastomes from a diverse range of 370 species encompassing 26 presently recognized genera. Employing a range of phylogenetic inference methods, including RAxMLIQ-TREE2 for Maximum Likelihood (ML) analyses, we established a robust phylogenetic framework for the Maleae tribe. Our phylogenomic investigations provided compelling support for three major clades within Maleae. By integrating nuclear phylogenetic data with morphologicalchromosomal evidence, we propose an updated infra-tribal taxonomic system, comprising subtribe Malinae Reveal, subtribe Lindleyinae Reveal,subtribe Vauqueliniinae B.B.Liu (subtr. nov.). Plastid phylogenetic analysis also confirmed the monophyly of most genera, except for Amelanchier, Malus, Sorbus sensu lato,Stranvaesia. In addition, we present a comprehensive taxonomic synopsis of Photiniaits morphological allies in the Old World, recognizing 27 speciesten varieties within Photinia, three speciestwo varieties within Stranvaesia,two speciesthree varieties within Weniomeles. Furthermore, we also lectotypified 12 namesmade two new combinations, Photinia microphylla(J.E.Vidal) B.B.LiuWeniomeles atropurpurea (P.L.Chiu ex Z.H.Chen & X.F.Jin) B.B.Liu.