Blast disease is one of the most important diseases of rice with the fungus Magnaporthe oryzae as the causal agent. This research was carried out to evaluate the blast resistance in aerobic rice genotypes in comparison with Iranian lowland rice cultivars as a randomized complete block design by measuring area under the disease progress curve (AUDPC) on 53 rice genotypes with three replications in 2017 and 2018 years. Furthermore, molecular evaluation was done using 30 genes-based markers and linked SSR markers along with 60 random SSR markers. According to the results, aerobic rice genotypes, IR82310-B-B-67-2, IR82589-B-B-114-3, IR82616-B-B-64-3, IR82589-B-B-84-3, and IR82635-B-B-143–1 (ranged from 4.11 to 5.96) and Iranian rice cultivars Nemat, Sange-Tarom and Sepidroud (ranged from 4.46 to 4.72) had the lowest AUDPC, indicating they had the least infection severity during different stages of the experiment. Iranian native rice cultivars showed the most susceptibility, and association analysis via stepwise regression showed a significant relationship between some of the markers and AUDPC. Two gene-based markers of Pi5 and Pib and RM259 were detected in accordance with previous studies, and eight SSR markers (RM12091, RM217, and RM3498 with positive effect along with RM234, RM276 RM1300, RM8007 and RM480 with negative effect) were identified as informative markers in relationship with AUDPC for the first time. RM12091 and Pi5 had the highest adjusted R 2 , accounting for 30.2% and 25.2% of AUDPC variation, respectively. The most effective identified markers could be considered in marker-assisted selection after final validation using different environments and genetic backgrounds. In addition, the results of this study can help demonstrate the significant potential of aerobic rice genotypes for resistance to blast disease.