Spot blotch, caused by Bipolaris sorokinaiana, is a major disease of wheat (Triticum aestivum L.) in warm humid regions of the world. The wheat association mapping initiative (WAMI) panel consisting of 289 diverse lines of wheat was phenotyped in 3 consequent years 2013–14 to 2015-16 under late sown (December) conditions at Agricultural Research Farm of Banaras Hindu University, Varanasi, India. A significant (P<0.05) differences was observed for Area Under Disease Progress Curve (AUDPC), plot yield, 1000-grain weight (TGW) and biomass among genotype, years and genotype × year. These 289 lines were genotyped at Genotyping Laboratory CIMMYT, Mexico using the Illumina iSelect beadchip assay for wheat having 9,000 SNPs. Markers with a minor allele frequency (MAF) <0.05 were excluded to avoid the high statistical power required to make meaningful statements about association with very rare alleles. Around 5,634 informative SNPs were selected and used for GWAS. Nine SNP markers on chromosomes 5A and 5B were significantly associated with resistance to spot blotch. Six were on 5B while 3 on 5A. The most significant associations for spot blotch AUDPC were on chromosome 5B (P = 3.9e-05). SNP markers significant associated with other traits were noted for TGW (3 SNPs on chromosomes 4D), plot yield (11 on 1A and 4D) and biomass (one marker on 6B). These SNP markers detected under late sown conditions could be useful for enhancing spot blotch resistance along with grain yield under warm humid environments of eastern Gangetic plains of South Asia.