The South American central Andes have a great richness of Asteraceae, where the genus Stevia (Eupatorieae, Piqueriinae) is also especially diverse. The taxonomy of Stevia species in the southern part of the central Andes pose a challenge because of the unclear delimitation among the species and overlap of morphological characters. Two species complexes were identified for the region comprising north Argentina and southern Bolivia. In this study, our objectives were to employ morphometric analyses to assess the delimitation of taxa within the Stevia alpina Griseb. and Stevia chamaedrys Griseb. complexes. We aimed to identify informative morphological characters and gain insight into the identity of species in each group. To accomplish this, we utilised cluster analysis, principal-component analysis, non-metric multidimensional scaling and univariate analyses to evaluate 37 morphological traits. In total, 200 specimens were examined, covering the entire geographic distribution of each species complex. We found support for the recognition of nine species: Stevia alpina, S. breviaristata Hook. & Arn., S. chamaedrys, S. mandonii Sch.Bip., S. mercedensis Hieron., S. minor Griseb., S. potrerensis Hieron., S. procumbens Hieron. and S. vaga Griseb. A new combination and status is proposed for S. tarijensis Hieron., incorporating it as a variety of S. mandonii, and S. centinelae Cabrera and S. crassicephala Cabrera are merged as synonyms under the name S. alpina. Two neotypes are designated for the names S. mercedensis and S. potrerensis.