Cryptantha Lehmann ex G. Don, an herbaceous plant genus of the Boraginaceae family, is found in western North America and western South America, but not in the tropics between. This amphitropical distribution has long puzzled scientists. In a previous study, Cryptantha was found to be paraphyletic and was split into five genera, including a weakly supported, potentially non-monophyletic Cryptantha. In all subsequent studies of the Amsinckiinae, the subtribe to which Cryptantha belongs, interrelationships of Cryptantha are generally not well-supported and have a low sample size. Next generation sequencing methods, such as genome skimming, allow for the acquisition of significantly more data at relatively low costs. Use of the complete ribosomal cistron, nearly complete chloroplast genome, and twenty-three mitochondrial genes, as well as a greatly increased sample size, has allowed for inference of relationships within this complex with strong support. The occurrence of a non-monophyletic Cryptantha is confirmed, with two clades, termed here the Albidae Clade and the Maritimae Clade, strongly supported as independent of the remainder of the genus. From these phylogenetic analyses, assessment of classification, character evolution, and the phylogeographic history that elucidates the current amphitropical distribution of the group, is performed. Revealing the timing, direction, and number of times of dispersal between North and South America gives insight as to the origin of the great biodiversity of these regions.