Nep Ngu rice is a valuable genetic of glutinous rice resource and cultural heritage with a long history of cultivation and utilization in Binh Dinh .A total of 102 traditional Nep Ngu varieties selectd at Binh Dinh province Vietnam, were used to explore this diversity using SSR markers and quantitative morphological characters. The study aims to evaluate the genetic diversity of Nep Ngu (Binh Dinh) varieties and involves molecular diversity analysis using 62 polymorphic SSR markers revealed among the 102 varieties. The Nep Ngu (Binh Dinh) varieties generated three clusters at 0.63 similarity coefficient. Some varieties with similar names were grouped into different clusters as molecular analysis showed that they were actually genetically different. The 102 Nep Ngu (Binh Dinh) varieties collected were evaluated phenotypically. In the analysis of quantitative traits, the range of coefficients of variability was high. It varied from 130.74-93.05 % (filled grain) to 30.38–18.16% (unfilled grain). This shows that these traits can be considered most stable as exemplified by their coefficients of variability. The highest values seen in unfilled grain indicate that this character is more affected by the environment and farmers’ cultural management practices. The mean values of quantitative trait measurements were higher (137.87–155.70 cm). The highest values noted in yield (36.33–56.52 g).Looking at agro-morphology, ANOVA showed highly significant differences among the 102 traditional rice varieties. The standardized Shannon-Weaver diversity indices for the quantitative morphological characters ranged from 0.68 to 0.89 with a mean of H’ = 0.79. Cluster analysis using UPGMA grouped the 102 traditional varieties into 3 major clusters. Varieties collected with two lines good for aroma with Line 81 and line 52. Sequence of Nep Ngu 52; Nep Ngu 81 were submitted to GenBank with accession number OR880900 and OR880901 respectively.