Tomato is a mild season crop and high temperature stress impacts productivity negatively. However, the development of cultivars with improved heat tolerance is possible as genetic variability has been consistently reported. This study aimed to identify candidate genes that impact various traits under heat stress. Genome-wide association studies (GWAS) were conducted on a diverse set of 144 tomato genotypes collected from various germplasm centers and breeding programs. The genotypes were grown under control and heat stress in poly tunnels having mean temperatures of 30°C and 45°C for two seasons and phenotypic data were collected on seven agro-physiological traits. All individuals were genotyped withthe80K DArTseq platform using 31237 SNP markers. Data were analysed using a mixed model based on restricted maximum likelihood (REML). Pattern analysis of the phenotypic data showed five primary clusters each with genotypes from multiple origins. Based on the genotypic data, three wild tomato genotypes showed a degree of un-relatedness with the other materials as they were distantly located from the rest of the genotypes in the scatter plot. Control treatment data were used to ascertain markers that are exclusively important under high temperature stress. A large number of markers were significantly associated with various traits under heat stress. These included strong marker associations for number of inflorescence/plant (IPP), number of flowers/inflorescence (FPI), fresh fruit weight (FFrW), and electrolyte leakage (EL). High association with EL was found due to two SNPs 7858523|F|0-25:G>A-25:G>A and 4705224|F|0-60:C>G-60:C>G located on Chr 6. Other less pronounced marker-trait associations were observed for plant dry weight (PDW), and number of fruit/plant (FrPP).