Spot blotch caused by Bipolaris sorokiniana is major constraint in wheat production in tropics and subtropics. The earlier work centered around, QTLs/genes identification using bi-parental mapping populations with limited power to detect polygenic trait due to lower marker density and genome coverage. In this study, we performed genome-wide association study (GWAS) for spot blotch disease resistance in spring wheat. The lines were evaluated under natural infection at Pusa Bihar and Jamalpur, Bangladesh, the hot spots for wheat spot blotch disease.The genotypes showed significant variation for disease severity at both the locations. Genotyping By Sequencing (GBS) method was used and 18637 polymorphic SNPs were included in the analysis. We identify 10 QTLs (p = <0.001) on chromosomes 1B, 2A, 2B, 3A, 3B, 4A, 4B, 5B, 6A, 7D. Most consistent QTL was on chromosome 2A detected across the locations and years. The results not only validates five QTLs on 2A, 2B, 3B, 5B and 7D identified in earlier studies but also provides highly associated SNP markers. The literature mining and BLAST of SNP tag sequence with wheat genome survey sequence database (IWGSC RefSeq) revealed that the QTLs on chromosome 1B, 3A, 4A, 4B, and 6A are novel. Gene annotation analysis of the candidate regions identified NBSLRR and 35 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and map based cloning to further characterize spot blotch disease resistance mechanism. Confirmation of previously identified genomic regions and identification of novel loci will facilitate improved understanding of spot blotch resistance and accelerate the disease resistance breeding efforts.