Rice (Oryza sativa L.) is a major staple crop supporting the livelihood and food security of more than half of the world’s population. However, at present drought stress is one of the most critical abiotic constraints affecting rice productivity, particularly in rainfed ecosystems. The present study was undertaken to assess the genetic diversity of 30 rice genotypes, including 23 indigenous cultivars from Manipur and 7 released varieties, were evaluated using 17 SSR markers associated with drought tolerance Quantitative Trait Loci (QTLs). Genomic DNA was extracted using the CTAB method and amplified through PCR. Out of the 17 markers used, 15 showed polymorphism and were used for further analysis. The polymorphic information content (PIC) values ranged from 0.50 to 0.78 with an average of 0.64, indicating that the selected markers were highly informative for diversity analysis. Genetic dissimilarity among the genotypes was estimated using Jaccard’s dissimilarity coefficient, which ranged from 0.19 to 0.98, demonstrating considerable genetic variation among the studied genotypes. The minimum dissimilarity was observed between Tomila and Hungyo, whereas the maximum dissimilarity was recorded between Shbhagi dhan and RCPL-17-1. Cluster analysis using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) grouped the 30 genotypes into four distinct clusters. Cluster I contained 8 genotypes including the drought-tolerant check Sahbhagi Dhan and MAS-26, while Cluster II, III, and IV comprised 7, 9, and 6 genotypes respectively. The results indicate that SSR markers linked QTLs associated with drought tolerance are effective tools for assessing genetic diversity in rice. The identified diverse genotypes can serve as valuable genetic resources for marker-assisted breeding programs aimed at developing drought-tolerant rice varieties for the rainfed ecosystems.