Amaranths belonging to family Amaranthaceae and genus Amaranthus is a C4 dicotyledonous herbaceous plants comprising approximately 70 species. The genus Amaranthus contains both cultivated and grain types, where cultivated ones are used for food grains, leafy vegetables, forage, ornamental gardening etc. Amaranth grains are pseudocereals containing high amount of proteins and minerals. Genetic diversity analysis of Amaranthus is important for development of core set of germplasm with widely diverse population and effective utilization of plant genetic resources. Several methods like use of morphological markers, molecular markers like proteins and enzyme based markers, ISSR, RAPD, AFLP, SSR, SNPs have been employed so far for genetic characterization of Amaranthus. In this study, we had core collection of 260 accessions from United State Department of Agriculture (USDA) and 33 accessions from Seed Savers’ Exchange (SSE). We evaluated morphological traits like blade pigmentation, blade shape, petiole pigmentation, branching index, flower color, stem color, inflorescence density, inflorescence shape, terminal inflorescence attitude, plant height and yield characteristics across all 293 accessions. We did genetic characterization of 276 accessions (249 accessions from USDA and 27 accessions from SSE) using KASPar designed 45 SNP markers. Data analysis of morphological data showed significant difference of petiole pigmentation, stem color, blade pigmentation, blade shape and flower color across different clusters of 260 accessions of USDA unlike among different clusters of SSE where we found significant difference of only blade pigmentation, blade shape and flower color across different clusters. The average yield per plant across 260 accessions of USDA and 33 accessions of SSE was 25.30g and 40.18g respectively. The SNP markers used were found to be highly polymorphic with an average PIC value of 0.5837 except one SNP marker (A-AM19583). The major allele frequency ranged from 0.3877 to 0.8533 with an average value of 0.6776. Model-based structure analysis with 100,000 burn-in length revealed the presence of highly polymorphic three populations with some admixtures across 276 accessions. The genetic relationship depicted by neighbor-joining method of DARwin software was consistent with the structure-based membership assignments of each accessions. This results will provide insights on germplasm conservation and crop improvement of amaranths
