Rice (Oryza sativa L.) is one of the important cereal grains and a staple food for more than 50% of the population in many countries. Increases in global temperatures will make crop productivity challenges worse. In this study, a total of 204 accessions from the Bengal and Assam Aus Panel (BAAP) were screened for resistance to heat stress. A total of eight replicate plants per accession were grown in the greenhouse until maturity; thereafter, five replicate plants were randomly selected, their panicles at anthesis stage marked and transferred to a large growth room at 38°C for 24 hours to assess high-temperature treatments. Three replicates plants were not heat treated. Fertility was assessed as the proportion of flowers filled. Genome wide association mapping was conducted using ~ 2 million SNPs. Two promising QTLs and 7 genes were detected for resistance under the ratio; which is the proportion of (control/heat treatment) on chromosome 2 and 6. The combine GWA mapping and RNA-seq allowed us to identify excellent candidate genes for heat tolerance in the aus subpopulation of rice. These genes were found in our significant QTLs on chromosome 2 and 6; Hsp20, SEC14, AP2/ERF, OsDjC56, ZOS6-06, WRKY28 and miRNA156. Altered fluorescence of detached leaves was also assessed under a 1 hr 47°C treatment. The two heat tolerance phenotypes were not correlated (P=0.193). This implies that leaf-level tolerance to high temperature is not genetically related to tolerance at the flowering stage.