The climate-resilient pseudocereal quinoa (Chenopodium quinoa Willd.) has enormous potential to enhance food and nutritional security in marginalized areas because of its nutritional richness, flexibility, and resistance to salinity and drought. The genetic diversity and molecular characterisation of eleven quinoa lines obtained from ICBA and other international institutes were investigated in this study. Polymorphism in 21 markers was found through genetic research using 40 InDel primers, which allowed accessions to be grouped into three groups according to characteristics including saponin concentration and yield potential. Important genetic resources were found to include saponin-free lines (Chen 254, D 11912, D 12406), genetically varied lines, and high-yielding lines (Co 407, BO 51). By establishing an indispensable molecular resource for quinoa breeding, our work speeds up the creation of sweet, high-yielding, and stress-tolerant varieties by facilitating marker-assisted selection (MAS). By combining genomics and traditional breeding techniques, quinoa will be able to spread into new agro-ecological zones, promoting sustainable agriculture and bettering public health, particularly in areas impacted by nutritional shortages and climate change. Keywords: Chenopodium quinoa, Molecular markers, Simple Sequence repeats.