Pathogens are imminent threats to crop production. Among the management tools available to protect crops from diseases, the use of host-plant resistance had been hindered by a lack of tools and resources to identify resistance genes (R-genes). Genomic technologies have empowered acquisition of a new level and quality of information on plant-pathogen interactions. Next generation sequencing, differential transcriptome analysis, gene editing, and use of bioinformatics have greatly expanded the numbers of R-genes identified, enriched understanding of R-avirulence gene interactions, and disease diagnosis. In this review, we highlight the application of genomic technologies to identification of pathogen machinery for future improvement of host plant resistance.