High temperature stress is an emerging threat to summer rice cultivation. In the present study, genetic diversity and population structure of 48 rice accessions of improved varieties and landraces were assessed by 35 microsatellite markers associated with high temperature stress tolerance. A total of 86 alleles were amplified with an average of 2.87 alleles per locus and their PIC values ranged from 0.0637 to 0.6799 with an average of 0.4105. The structure software grouped the total rice accession into two distinct sub-populations. The Fst values of the two populations were 0.0081 (population 1) and 0.3272 (population 2). The allele frequency divergence between two populations was 0.0814. The phylogenetic analysis grouped the genotypes into two major clusters and 3 sub-clusters. Clustering based on polymorphic high temperature stress tolerance linked SSR markers classified the total rice accessions mainly into 2 clusters.