Amaranth (Amaranthus caudatus L.) is an important pseudocereal in the Andes. The seed has excellent nutritional value (high in protein, essential amino acids, and minerals) and ample capacity for growth in diverse, harsh Andean subsistence-production conditions such as water deficiency, salt stress, and soil mineral nutrient deficiency. The objective of this study was to characterize and quantify the genetic diversity among a series of 178 mostly Peruvian amaranth genotypes using 96 biallelic single-nucleotide polymorphism (SNP) markers. A total of 96 co-dominant, biallelic markers were developed using KASPar™ assays on a 96.96 Fluidigm EP1 array system. The 178 amaranth genotypes included white-opaque and white-translucent (vitreous) putative A. caudatus seed types, along with black-seeded A. hybridus and brown-seeded types, all isolated from among 48 accessions of the CICA-UNSAAC collection. Variation among and within samples and accessions was compared for empirically determined clusters (northern, north-central, south-central, and southern Peruvian Andes). Variation was highest within samples for all groups, but only in white-seeded amaranth was the p-value significant (17.43). The greatest variation among samples was found in the vitreous-seeded group (99.35). The highest average observed heterozygosity within-groups (Ho) was 0.19 in the brown-seeded group, and expected within-group heterozygosity (He) was highest in the vitreous-seeded group (0.359). Cluster analysis (UPGMA), PCA and PCO results partitioned the amaranth accessions into six discrete clusters. Clusters did not manifest obvious structure among accessions, which indicates that genetic diversity has been conserved across a broad region of the Peruvian Andes. The diversity characterization pointed to a center of origin and domestication of A. caudatus in the Ayacucho-Cusco region of southern Peru.