<p>Grain amaranth (<i>Amaranthus hypochondriacus</i> L.) is a gluten-free pseudocereal with high nutritional value and notable climate resilience; however, its genome-wide population structure and genetic diversity remain poorly characterized. Given the considerable diversity observed in its gene pool, comprehensive genome-scale characterization are required to understand the genetics of important traits for effective breeding and improvement. Here, we employed Whole-Genome Sequencing (WGS) approach to generate genome-wide SNPs in a core accessions of <i>A. hypochondriacus</i>, leveraging the available reference genome. A total of 248 accessions, comprising Indian and some exotic accessions, were sequenced through Illumina paired-end sequencing, yielding 285,236 high-quality SNPs, with an average of ~ 20 × genome coverage. Population structure analysis identified six sub-populations among the core accessions, consistent with kinship and phylogenetic analyses, reflecting substantial genetic diversity within the genetic material used. Linkage disequilibrium (LD) analysis indicated moderate genome-wide LD, with an average decay distance of 29.8&#xa0;kb, although strong LD (r² ≥ 0.8) was observed in some marker pairs. Functional annotation of 17,350 SNP-associated genes revealed enrichment of loci related to metabolic processes, stress responses, and developmental pathways, providing biological context observed genomic variation. Further, several genetically diverse accessions identified in this study offer valuable resources for future breeding efforts. Together, these results establish a robust genomic framework for <i>A. hypochondriacus</i> that supports future genome-wide association studies and genetic improvement efforts in grain amaranth.</p>