Chenopodium pallidicaule, known commonly as cañahua, is a semi-domesticated crop grown in high-altitude regions of the Andes. It is an A-genome diploid (2n = 2x = 18) relative of the allotetraploid (AABB) Chenopodium quinoa and shares many of its nutritional benefits. Both species contain a complete protein, a low glycemic index, and offer a wide variety of nutritionally important vitamins and minerals. Due to its minor crop status, few genomic resources for its improvement have been developed. Here we present a fully annotated, reference-quality assembly of cañahua. The reference assembly was developed using a combination of established techniques, including multiple rounds of Hi-C based proximity-guided assembly. The final assembly consists of 4,633 scaffolds with 96.6% of the assembly contained in nine scaffolds representing the nine haploid chromosomes of the species. Repetitive element analysis classified 52.3% of the assembly as repetitive, with the most common (27.3% of assembly) identified as LTR retrotransposons. MAKER annotation of the assembly yielded 22,832 putative genes with an average length of 4.6 Kb. When compared with quinoa, strong patterns of synteny support the hypothesis that cañahua is a close A-genome diploid relative, and thus potentially a model diploid species for genetic analysis and improvement of quinoa. Resequencing and phylogenetic analysis of a diversity panel of 30 cañahua accessions collected from across the Altiplano suggests that coordinated efforts are needed to enhance genetic diversity conservation within ex situ germplasm collections.