This study reports a new species of Domeykoa (Apiaceae; Azorelloideae) from the Andes of northern Chile. A detailed description and an illustration of the species are provided. Diagnostic morphological characters that distinguish it from similar species are its erect habit, fewer flowers per umbel, and opposite leaves. The new species is an erect annual or short-lived perennial herb, it is glabrous, up to 25 cm high, and is profusely branched close to the base. Its umbels are simple, sessile, or sub-sessile with three or four yellow flowers. DNA was obtained for molecular phylogenetic analyses. Bayesian analyses showed that the new species, D. andina, is nested within the previously recognized Clade Eremocharis-Domeykoa, as sister to D. amplexicaulis from the southern coast of Peru. This study confirms previous findings that neither of the two genera in the clade are monophyletic, raising questions about the nomenclature. The phylogeny also suggests an interesting Peru-Chile latitudinal disjunction of more than 500 km, also seen in other recently described species. However, a more complete phylogeny is needed to make conclusions on this matter. Based on IUCN criteria and categories, we suggest assigning a critically endangered (CR) category to Domeykoa andina.