Genetic diversity among 30 upland rice genotypes (Oryza sativa L.) was evaluated using morphological and SSR markers. Roger’s distance was calculated for all the data sets as a measure of genetic distance between accessions. The distance matrices were used to generate a dendrogram based on the UPGMA method. The minimum genetic distance based on morphological marker was 0.04 which was found between Megha Rice-1 and Megha Rice-2. 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. Polymorphism information content (PIC) values ranged from 0.062 to 0.799 per locus with an average of 0.425. 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. In cluster analysis, morphological and molecular 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 Poireiton, 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 which may be used as parent for hybridization during further rice improvement.