A new Schizanthus species from northern Chile is described and illustrated. Schizanthus nutantiflorus was discovered based on recent collections made during unusual rain events in the Atacama Desert in 2015. The new species is distinguished morphologically from other Schizanthus species from northern Chile by its short corolla tube, with a distinct upper lip arrangement and colour, having the longest lower lip, and downward-facing flowers. Additionally, the reinstatement of Schizanthus fallax is proposed. By using both nDNA and cpDNA, phylogenetic relationships among all species of Schizanthus were investigated. Molecular and field observations, as well as an exhaustive morphological revision of fresh material and herbarium specimens, supports the segregation of Schizanthus with short corolla tubes from northern Chile into three species. We propose that, in order to fully understand both the taxonomy and evolution of Schizanthus, an integrative framework encompassing molecular, ecological, and morphological data should be carried out. Information on distribution, habitat, informal conservation status, as well as taxonomic notes and illustrations are provided. In addition, an updated key for the species of Schizanthus from northern Chile is given.