In this comprehensive study, based on extensive taxon sampling, we performed phylogenomic analyses of plastomenuclear ribosomal DNA (nrDNA) datasets. We employed multiple inference methods, including concatenatedcoalescent-based strategies, to generate an accurate phylogeny of the woody Rosaceae genus Pourthiaea. The nrDNA phylogeny of Pourthiaea strongly supports three major clades, which are consistent with morphology. However, the plastid tree provides an alternative phylogenetic topology, indicating cytonuclear discordance which could be explained by frequent hybridizations betweenamong the species of Pourthiaea. Considering evidence from morphologyphylogenomic data, we propose a new infrageneric classification for Pour_x005fthiaea, consisting of three sections: P. sect. Pourthiaea, P. sect. Amphidoxae sect. nov.,P. sect. Impressivenae sect. nov.