Genetic diversity among 30 upland rice genotypes (Oryza sativa L.) was evaluated using 28 morphological markers and 20 SSR markers. The 30 genotypes included the 24 landraces, 4 improved lines and two Gene Bank lines. The morphological characteristics and their states given as per the National Test Guidelines for Distinctness, Uniformity and Stability (DUS) of rice were recorded at different stages of crop growth period and scored in codes ranging from 1 to 9. Among all the genotypes evaluated, Mapuma and Aizawng New have the highest (134.7 cm) and shortest (49.3 cm) mean stem length, respectively. Leaf ligules were present in all the genotypes varying from white to yellowish (Megha Rice-1 and Megha Rice-2) and purple (Chakhao Poireiton and Lokhumo (Tall)) colour. On the basis of 50% flowering, thirteen genotypes showed medium (91-110 days) flowering, nine genotypes (Chingi Chakhao Angoubi, Lamyang, Zon-Chou, Mapuma, Tungou, Kobra, Shomboro Epyu, Marow and IC 583137) showed late (111-130 days) flowering and eight genotypes (Keibi Phou, Chakhao Poireiton, Nobi Chamoro, Aizawng New, KbaLumiong, Bhoi, Kba Tlang, IC 583129) showed very late (> 130 days) flowering. Megha Rice-1 and Megha Rice-2 have the highest panicle length with 37.925 cm and 35.185 cm respectively while Chakhao Poireiton and Aizawng New have the shortest panicle length with 17.74 cm and 17.8 cm respectively. Kobra had the largest number of panicle per plant with mean of 16.8 panicles/plant. Seed weight ranged from 18.8 g (Chakhao Poireiton) per 1000 seeds to 36.8 g (Shomboro Epyu) per 1000 seeds. The minimum genetic distance based on morphological marker was 0.04 which was found between Megha Rice-1 and Megha Rice-2 showing their close relationship to each other. The maximum genetic distance was 0.75 observed between Aizawng New and Majinlu, Aizawng New and Mima-Mitong-Jang, Mibisa and Chakhao Poireiton, Chakhao Poireiton and Vepvu Tsuk with an average of 0.395. The number of alleles per SSR marker varied from 2 to 8, with an average number of 4.286 alleles per locus. Polymorphic informationcontent (PIC) values ranged from 0.062 to 0.799 per locus with an average of 0.425. Variability among groups (FIS=0.727) and variability within individuals (FIT=0.756) were low due to high fixation index of the alleles. However, there was high variability among the individual genotypes within groups due to low fixation index of the alleles (FST=0.108). The minimum and maximum genetic distances based on Roger’s distance, were found to be 0.00 (Bhalum-1 and Bhalum-2) and 0.84 (Aizawng New and Mibisa) respectively, with an average of 0.42. In cluster analysis, morphological and marker-based genetic distance grouped the local landraces together with the improved lines and Gene Bank lines. Correlation analysis between morphological data and molecular data revealed a very poor association (r=0.051 at p=0.271). The diverse genotypes revealed from morphological-based dendrogram were the following pairs viz., Aizawng New and Majinlu, Aizawng New and Mima-Mitong-Jang, Mibisa and Chakhao Poireiton, Chakhao Poireiton and Vepvu Tsuk, Buh Pui (Tuirel) and Chakhao Poireiton, Marow and Chakhao, Kba Tlang and Majinlu, Lokhumo (Tall) and Chakhao Poireiton. While Aizawng New and Mibisa, IC 583129 and Mibisa, Bhalum-1 and Mibisa, Bhalum-2 and Mibisa, Marow and Mibisa pairs were identified as the diverse genotypes based on molecular dendrogram.