Domesticated populations of the South American grain chenopod quinua (Chenopodium quinoa subsp.quinoa) have been formally classified on the basis of pigmentation and inflorescence morphology, and informally grouped according to ecotypic variation. Comparative analysis of morphometric and electrophoretic data taken from 98 populations reveals two fundamental elements: a coastal type from southwestern Chile and an Andean type distributed at elevations above 1,800 m from northwestern Argentina to southern Colombia. Andean quinua can be further divided into northern and southern groups, with the northern populations weakly marked by broad, unlobed leaf blades, sharply margined fruit, and relative uniformity. With the exception of allozymes unique to coastal quinua, characteristics that differentiate populations from the Chilean coast and the northern Andes represent a subset of variation present in the southern Andes. This could reflect diffusion from a possible center of origin in the southern highlands. Overall phenetic association places populations from the Altiplano of Peru and Bolivia in a central, linking position. The high genetic identities among all quinua populations argue against a polyphyletic origin for the crop and specific differentiation among cultivar groups. The overall pattern of variation supports the ecotypic approach toward landrace classification of quinua, although congruence between ecological and morphogenetic variation is not complete. While genetic diversity is clearly centered in populations of the southern Andes, conservation efforts should focus on well differentiated quinua populations at the poorly marked northern and southern extremes of distribution.