Recent taxonomic treatments of the genus Harpagonella have included only one lower taxon, Harpagonella palmeri A. Gray. However, a larger-fruited variety of Harpagonella palmeri from Arizona and Sonora was described by I.M. Johnston in 1924. He continued to recognize this taxon - Harpagonella palmeri var. arizonica - in his treatment of the genus in Kearney and Peebles's Arizona Flora in 1960. Here, we provide two lines of molecular evidence and quantitative morphological evidence from calyx characters showing that plants of Harpagonella from Arizona, Sonora, and central Baja California, corresponding to Johnston's var. arizonica, are distinct from Harpagonella palmeri of southern California and Baja California. We make the new combination Harpagonella arizonica (I.M. Johnston) Guilliams & B.G. Baldwin, comb. nov. for the plants from Arizona, Sonora, and central Baja California.