The trait of resistance or tolerance to specific pathogens is pivotal for crop resilience, mitigating losses without resorting to excessive chemical treatments. The identification of genes imparting resistance to a particular disease demands sophisticated mapping approaches. Genome-wide association studies (GWAS) involve scanning an organism’s genome using hundreds of thousands of genetic markers to test the association of a specific genomic region with resistance to a pathogen. This is particularly beneficial for controlling soil-inhabiting and insect-transmitted pathogens that are challenging to manage with chemicals. GWAS can also unveil virulence genes in pathogens, although it lags a few steps behind. Compared to traditional linkage-based QTL mapping, GWAS offers advantages by significantly reducing the time required for fine mapping for resistance to a pathogen. It also aids in identifying whether complex epistatic networks govern the expression of the trait of interest. With the prevalent availability of sequence information for most crop species and a decrease in genotyping costs, GWAS has become the most preferred method for targeting specific resistance loci. The ensuing literature delves into the methodology of GWAS through case studies, outlines the advantages and disadvantages of GWAS, and explores its application in identifying pathogenicity factors in microbes.