Megacodon is an ideal genus to study speciation and ecological adaptation in the Sino-Himalayan region. The genus contains two species distributed at different elevations and in two separate areas. However, studies of this genus have long been impeded by a lack of fieldwork on one of its species, Megacodon venosus. In this study, we collected specimens of two Megacodon species and found an extraordinary new species of Megacodon in Lushui county of north-west Yunnan province, which we have since named Megacodon lushuiensis. We propose new species based on both morphological and molecular evidence. The finding of this new species emphasized the importance of ecological divergence in the divergence of Megacodon stylophorus and its parapatric low-elevation Megacodon species. To identify genetic de-terminants that underlie adaptations to different elevations, we characterized transcriptomes of the new species M. lushuiensis, which is distributed at low elevations, and M. stylophorus, which is distributed at high elevations. Comparative transcriptome analysis identified 8926 orthogroups containing single-copy genes, and 370 orthogroups containing significantly positively selected genes. The set of positively selected genes was enriched into 25 Gene Ontology terms, includingresponse to water deprivation,response to osmotic stress, andcellular response to extal stimulus. Our results provide new in-sights into how ecological adaptation and speciation occurred in Megacodon and highlight the role of heterogeneous habitats in the speciation of plants in the Sino-Himalayan region.