The brown planthopper (BPH) is predominant rice insect pest of Asia. Identification of novel and diverse germplasm to combat BPH is inevitable, due to breakdown of resistance. The phenotypic screening was performed at IRR, PJTSAU, Rajendranagar, Hyderabad, India during kharif 2020 and 2021. Out of 300 genotypes (3k subset panel of BPH) and eight checks tested in field, two genotypes viz., IRGC 126266 and IRGC 128206 exhibited resistant reaction (3.0) and moderate resistance to BPH (5.0) at seedling stage. IRGC 126266 displayed all three resistance mechanisms viz., antixenosis, antibiosis and tolerance, with lower honey dew excretion (72.5 mm2), lower nymphal survival rate (47.5%), longer nymphal development period (17.20 days), lowest GI (2.70) and > days to wilt (27.2 days), compared to TN1 (165.7 mm2, 67.5 %, 12.7, 5.30 and 13.7 days, respectively). A total of 42,304 cured SNPs and phenotypic data (kharif 2020, 2021 and across the years) were used to identify MTAs. GWAS analysis was performed using four single locus models (GLM, MLM, CMLM and ECMLM). A total of 39 and 28 MTAs were identified on different rice chromosomes for BPH population/hill and BPH damage score, respectively. Candidate gene analysis was performed within the LD block and revealed that 10 and 9 MTAs were associated with stress tolerance genes for BPH population and BPH damage score, respectively. Simultaneously, the two identified germplasms were genotyped using SSR markers. The marker RM 16994 linked to Bph 34 gene was observed in both BPH resistant lines viz., IRGC 126266 and IRGC 128206, whereas the SNP identified in the locus (LOC_Os04g53510.1) is associated through GWAS was 10 Mb away to Bph 6 and Bph 34 found to encode a LRR protein. The robust marker RM 190 and flanking marker RM 3726 – RM 5479 indicated the presence of Bph 3 and Bph 21 genes, respectively in IRGC 126266. For IRGC 126266 through GWAS, a significant SNP was identified in the locus (LOC_Os06g50370.1) just located 0.4 Mb away from Bph 3 and another SNP (LOC_Os12g37970.3) within this region of Bph 21. The findings disclosed that the two lines viz., IRGC 126266 and IRGC 128206 could be new potential donors for breeding and developing high yielding rice varieties with durable BPH resistance.