Reticulate evolution, driven by incomplete lineage sorting (ILS) and gene flow, is increasingly recognized as a fundamental process shaping lineage diversification, posing both challenges and opportunities for taxonomic treatment. During field investigations in Xizang, China, we discovered a morphologically distinct new species exhibiting certain similarities with the genera Microtoena yet clearly differing in corolla morphology. We sampled all 12 currently recognized genera within the tribe Pogostemoneae and conducted phylogenomic analyses integrating data from 539 low-copy orthologous nuclear genes (ONGs) and complete plastome sequences to clarify the systematic position of this new species. Our analyses revealed that this species forms a sister group relationship with Microtoena griffithii, previously treated as synonymous with M. moupinensis. The nuclear phylogeny resolved this lineage as sister to the remaining Microtoena species, whereas plastid-based trees presented an alternative topology. Integrating macromorphological, micromorphological, and molecular phylogenetic evidence, we herein describe the new genus Paramicrotoena and propose a new species and a new taxonomic combination. The newly established genus Paramicrotoena can be distinguished from the other 12 genera within the tribe Pogostemoneae by several distinctive morphological traits, including notably longer bracts, shorter corollas, a laterally reflexed upper corolla lip that exposes the stamens, and the presence of a hairy annulus at the base of the corolla tube. Furthermore, we reconstructed a robust and well-supported phylogenetic framework for the Pogostemoneae and investigated phylogenomic discordance and reticulation within Microtoena and Paramicrotoena. Conflict analyses demonstrated that ILS and gene flow collectively explain widespread nuclear gene-tree discordance, likely promoting both the origin and diversification of Microtoena through ancestral lineages closely related to extant species of Paramicrotoena.