To identify associated agronomic traits and quantitative trait loci (QTLs) with high-temperature tolerance in rice (Oryza sativa L.), three backcross inbred populations (BC₂F₄) of NSIC Rc150/Dular, Gayabyeo/Nagina22 and Gayabyeo/Dular were screened during the 2014 dry season. Analysis of microclimate conditions of near canopy such as temperature, relative humidity, and dew point temperature using Micrometeorological Instrument for Near Canopy Environment of Rice (MINCER) confirmed the presence of high-temperature stress during heading and maturity stages. MINCER data showed high temperatures (37.04 ± 0.14°C), accompanied by dry to high humidity (89.00 – 35.03 ± 1.82%) condition. Pearson correlation and multiple linear regression analysis were used to evaluate phenotypic traits associated with fertility. Dehiscent high-temperature was correlated with spikelet fertility in NSIC Rc150/Dular and Gayabyeo/Nagina22. Number of spikelets showed significant correlation with fertility in the cross between Gayabyeo/Nagina22 and Gayabyeo/Dular. The variability explained by the associated traits to the high-temperature tolerance in NSIC Rc150/Dular was 56%, which was higher than the variability (54.00%) in Gayabyeo/Dular populations. The lowest variability (40.00%) explained by the associated traits was observed in Gayabyeo/Nagina22. In a previous study, QTLs were identified on chromosomes 1, 3, 4, 5 and 10 (Grospe et al. 2016). This study further identified QTLs in different mapping populations using the inclusive composite interval mapping (ICIM) method with IciMapping 4.0 software. Four major QTLs, which were associated with high-temperature tolerance in the new mapping population of Gayabyeo/Dular, were identified, namely qHTfert3 (17.50%), qHTtof10.1 (14.10%), qHTtof10.2 (15.20%) and qHTspk4 (15.35%). Rice Genome Browser was used to identify the neighboring and coincided genes with the identified QTLs. The co-located/coincided/co-located genes in NSIC Rc150/Dular were qHfert1 (RM9) - LOC_Os01g41200, qHTfert3 (RM16238) - LOC_Os03g64190, qHTfert4 (RM348) - in LOC_Os04g54890, qHTtof10 (RM25213) - LOC_Os10g18740, qHTdht3 (RM16238) - LOC_Os03g64190, qHTdht3 (RM3586) - LOC_Os03g63950, qHTdht4 (RM16742) - LOC_Os04g28100, qHTdht5 (RM480) - LOC_Os05g47660, qHTdht10 (RM25213) - LOC_Os10g18740, qHThd3 (RM16102) - LOC_Os03g59480, and qHThd3 (RM16238) - LOC_Os03g64190. The co-located/coincided/co-located genes in Gayabyeo/Dular were qHTtof10.1 (RM4455) - LOC_Os10g22510 and qHTspk4 (RM17486) - LOC_Os04g52300. This study inferred that QTLs for high-temperature tolerance are cross specific, hence QTLs varied depending on parental combination. Moreover, these can be used in fine mapping of novel genes and rice breeding in marker-assisted selection (MAS) for high-temperature tolerance in rice.