A laborious and difficult task in current tree of life reconstruction is to resolve evolutionary relationships of closely related congeneric species that originated from recent radiations. This is particularly difficult for forest species with long generation times and large effective population sizes such as conifers. As the species diversity center of Picea, the Qinghai-Tibetan Plateau (QTP) and its adjacent areas harbor 11 species (including 5 varieties) of this genus, but evolutionary relationships of these species are far from being resolved due to recent radiation, morphological convergence, and frequent interspecific gene flow. In this study, we use these spruce species to test whether phylotranscriptomic analysis, combined with population genetic analysis, can disentangle their evolutionary relationships, and to explore whether reticulate evolution has occurred among them. Phylogenomic analyses indicate that all spruce species in the QTP and neighboring areas, except P. asperata and P. crassifolia, cluster together, and in particular, nearly all taxa (including varieties) form their own monophyletic groups, although the two species P. likiangensis and P. brachytyla are not monophyletic. We found that, compared to herbaceous plants, many more genes (a minimum of 600 OGs for Picea) are required to resolve interspecific relationships of conifers. Our study does not support a hybrid origin of P. purpurea reported in previous studies, but suggests a hybrid origin for P. brachytyla var. brachytyla and P. likiangensis var. rubescens. Moreover, we emphasize that population genetic and phylogeographical studies should sample a monophyletic group if more than one species are involved.