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L. is a relatively under-studied genus that includes the cultivated seed crop quinoa ( Willd.). Quinoa is an allotetraploid (2 = 4 = 36, AABB genomes) that is cultivated by subsistence farmers and commercial growers in the Andean regions of South America. Approximately 60% of a quinoa seed is starch, a glucose polymer that is an important carbohydrate energy source in the human diet. Seed starch is normally composed of amylose and amylopectin in a 1:3 ratio. The accumulation of the amylose fraction of starch is controlled by a single dominant gene in quinoa, . We report the sequencing and characterization of the gene in 18 accessions of , including Andean quinoa and the related Mesoamerican chenopod domesticate, subsp. Saff. Two distinct homeologs ( and ) were identified in the tetraploid accessions, and 19 different alleles were identified, including three null mutants—one in an accession of quinoa and two in a waxy landrace of subsp. . Expression analysis of the null mutants revealed that and were both strongly expressed late in seed development. sequences were used to analyze the phylogenetic relationships between quinoa and other members of the genus. This study and the discovery of null-mutants will assist in the development of new crops with novel starches.