Quinoa (Chenopodium quinoa Willd.) stands out as a versatile cereal crop, celebrated for its exceptional nutritional content and medicinal properties, as well as a wide range of morphological and genomic variations. Despite numerous studies on the genetic diversity of quinoa germplasm, a comprehensive assessment remains insufficient. In contrast, research focusing on the DUS traits and molecular variation in the germplasm used in China is relatively limited. We thoroughly examined 170 quinoa accessions, focusing on 30 morphological characterizations based on DUS descriptors (referred to as DUS testing traits) and 23 simple sequence repeat (SSR) markers. The results indicated that all 30 DUS testing traits were polymorphic. In total, we detected 136 allelic variations across the 170 varieties, averaging 4.53 per trait. The average Shannon index (I) was 0.97, with values ranging from 0.09 to 1.67. Diversity was highest at T30 (Time of maturity) and lowest at T6 (Stem: color). Using the UPGMA (unweighted pair-group method with arithmetic means) method, the cultivars were classified into three distinct groups, a categorization further supported by principal component analysis. To streamline field identification and screening, 18 key traits were identified based on principal component scores. Furthermore, the genetic diversity of all materials was analyzed using 23 SSR markers. The analysis revealed an average of 11.185 observed alleles, 3.874 effective alleles, a Nei’s gene diversity index of 0.680, and a Shannon’s information index(I) of 1.547, highlighting the substantial genetic diversity within the population. Subsequent genetic structure and DAPC (Discriminant analysis of principal components) analysis divided the population into four subgroups, reflecting the cluster analysis results. Notably, a significant portion of total genetic variation (58.033%) existed among individuals, with 26.289% among subgroups. The analysis also showed a notable degree of gene flow variation, with an estimated Nm value of 0.701, underscoring the genetic diversity among the quinoa cultivars studied. The use of a comprehensive set of 23 SSR markers, alongside DUS traits, proved highly effective in accurately distinguishing the tested quinoa cultivars. This robust method provided valuable insights that could significantly contribute to conserving quinoa genetic resources and enhancing their use.