Meedon rice varieties are important for local adaptability, grain quality and market availability, and have been grown in Myanmar for centuries. Because of temporal variability and spatial heterogeneity, Meedon rice varieties in rainfed lowland areas may be diverse. However, information on diversity of Meedon rice germplasm is limited. This study was carried out to assess genetic diversity and to analyze population structure of Meedon rice germplasm conserved in Myanmar Seed Bank using SSR markers. For assessing genetic diversity, 154 accessions of Meedon rice germplasm were analyzed with nine SSR markers. A total of 86 alleles were detected with an average of 9.6 alleles per locus. All the loci were found to be polymorphic, and there were considerable genetic variation among accessions with mean values of expected heterozygosity (HE) = 0.5774 and polymorphic information content (PIC) = 0.5496. High frequency of rare alleles was identified, among which 35 unique (accession-specific) alleles were observed. Based on cluster analysis, rice accessions were mainly clustered into two groups, and as a result of model-based analysis, two distinct genetic populations and an admixture were classified. This result indicated that SSR markers have proved to be useful markers for detecting genetic diversity in Meedon rice, and the occurrence of a considerably high number of rare and unique alleles in the germplasm indicates their potentiality as a reservoir of rare genotypes for use. Unique alleles are also important because they may be diagnostic of a particular type of genotype for identification.