Meconopsis is an herbaceous genus native to the high altitude habitats across the Himalaya and adjacent plateau and mountain areas. Attractive Meconopsis flowers have spurred many European botanists to study the taxonomy of the genus resulting in numerous infrageneric classifications, dating from the first taxonomic revision in the late 19th century until the most recent monograph in 2014. All, however, were morphology-based treatments and largely inconsistent with one another. To investigate the incongruence among the previous taxonomic grouping strategies of the species in Meconopsis and settle the controversies, we employed a well-resolved molecular phylogeny built by analyzing four chloroplast markers (trnL-trnF intergenic spacer, matK, ndhF, and rbcL). We found that the evolutionary relationships revealed by our phylogeny disagreed to varying degrees with any infrageneric relationship suggested by previous authors. Therefore, we propose a revised classification based on our phylogenetic topology aswell as themorphological and cytological patterns reflected by the phylogenetic structure. To achieve a practical and approachable system, we have tried to retain as much as possible of phylogenetically meaningful components from previous taxonomies for the genus. As a result, we used the four major clades of our Meconopsis phylogeny as the bases for infrageneric sections (Meconopsis sect. Meconopsis, M. sect. Aculeatae, M. sect. Primulinae, and M. sect. Grandes). A key to the sections is provided, followed by a description and composition of each.