The mountains of southwest China are one of the hot spots of biodiversity in the world. However, the high-altitude fauna that inhabit these mountains remain a mystery. In this study, the species diversity of the aphids of the genus Cinara from the high-altitude coniferous forests was first assessed, and then the processes and the mechanisms of speciation were discussed. Three hundreds and four aphid samples that contained 3040 individuals were collected during fourteen field surveys. The molecular clusters derived from the DNA barcodes were used to explore the species diversity. Notably, the aphid alpha-diversity was high, with as many as 94 candidate species, and furthermore, 86.2% of the species collected had not been previously recorded. The centers of aphid species richness corresponded to the distributional pattern of the diversity of the host conifer plant species. The divergence time revealed that following the uplift of the Qinghai-Tibetan Plateau during the Pleistocene, the changes in the climate, ecology and host habitats were likely the most important factors that drove the rapid process of evolutionary radiation in the aphids. Our findings revealed the high species diversity of the aphids with DNA barcoding.