<p>Amaranthus is a major leafy vegetable, and India is centre of its diversity. To assess variation within the Indian germplasm, 96 Amaranthus genotypes were evaluated using an augmented block design, scoring 20 morphological descriptors and analyzing DNA-based diversity with inter-simple sequence repeat (ISSR) and simple sequence repeat (SSR) markers. All morphological traits showed a wide range of variation, including rare or unique phenotypes such as novel leaf shapes, white and pink stems, petiole pigmentation, and distinct inflorescence colour patterns. Shannon-Weaver indices ranged from 0.00 to 1.48, with 11 traits showing significant morphological variation. Molecular analyses revealed considerable polymorphism, with six of thirteen ISSR markers and nine of twenty-two SSR markers being polymorphic. Analysis of genetic diversity showed low within-population diversity (Hs = 0.15) but higher total diversity across populations (Ht = 0.26), along with moderate-to-high differentiation (Gst = 0.42) and low gene flow (Nm = 0.34), indicating strong population structuring. Principal coordinate analysis revealed substantial genetic variation, partial population clustering, and evidence of admixture, while marker-based clustering divided the collection into five clusters. Population structure analysis further identified four admixed subpopulations, highlighting the complex genetic relationships within the germplasm. These findings demonstrate structured and exploitable variation in Indian Amaranthus, providing a basis for selecting diverse parental lines, broadening the genetic base through compatible crosses, and supporting crop improvement programs.</p>