Gomphrena meyeniana is an extremely variable species from the Andean highlands, which has attracted the attention of many botanists because it is the world's highest-elevation C₄ eudicot and because of its wide morphological variability. It has the typical high-Andean plant morphology, with small leaves tightly clustered on a thick rootstock. The large range of morphological variation within this species coupled with the varying opinions on the existence of several species or infra-specific taxa and the lack of molecular information has made the clarification of the G. meyeniana complex a challenge. Our approach was to perform broad molecular sampling to identify the phylogenetic position of G. meyeniana within Gomphrena and to perform a multivariate analysis to objectively differentiate taxa based on morphological characters. The ITS and trnL-F regions were analyzed individually and in combination using Bayesian inference and maximum parsimony methods. To analyze the morphological characters we performed a clustering method (partitioning around medoids with the Gower's dissimilarity algorithm). The molecular analyses supported the monophyly of the G. meyeniana complex, but did not support segregation into varieties. The morphological analyses supported recognition of three varieties that can be easily distinguished by three simple characters: the presence of leaves on the flowering shoot, the habit of the flowering shoot, and the pilosity of the sepals. The varieties of G. meyeniana accepted here are G. meyeniana var. meyeniana, G. meyeniana var. caulescens, and G. meyeniana var. flaccida. A dichotomous key to identify the infra-specific taxa is here presented and illustrated. Gomphrena meyeniana var. tucumanensis and G. meyeniana var. conwayi are synonymized with G. meyeniana var. caulescens and G. meyeniana var. meyeniana, respectively.