Soybeans are among the world’s main crops because they are excellent sources of proteins, micronutrients, and oil. Considering that abiotic stress affects agribusiness, resulting in losses, the grain yield of the crop must be maintained even at high temperatures. In this context, the objective of this study was to select markers related to soybean yield assessed under high temperatures, using associative mapping. The mapping population included 80 soybean PIs and 15 controls. For phenotyping, genotypes were evaluated at high temperatures in an experiment conducted in Teresina (in the state of Piauí) and four characters of interest for agronomy were evaluated: height of the plant when mature, agronomic value, 100-seed weight, and grain yield. Genotyping was carried out using the Affymetrix Platform (180 K Axiom® Soybean Genotyping Array), and the imbalance in the connection between pairs of markers was calculated through the coefficient of determination using the fast permutation test. The analysis of the association between markers and the phenotype of interest was carried out using a generalized linear model approach, including phenotyping data, SNP markers, and information on population structure. The results revealed that 34.06% of loci showed a significant linkage disequilibrium (p < 0.001), and 16 significant associations were found for the four characters related to heat tolerance. These associations can aid breeders that aim to incorporate high temperature tolerance in programs of soybean genetic improvement via selection assisted by markers.