Information technology and biology are connected through the field of bioinformatics, which aims to analyze molecular data by computational methods. Bioinformatics is essential to many areas of agricultural research, such as breeding, crop development, and plant pathology. The bioinformatics-based applications allow the processing of vast amounts of complicated molecular biological data for annotation and uncover new information associated with the data. Plant scientists frequently employ bioinformatics tools, methods, and databases to find putative genes and target proteins in host–pathogen interactions and disease resistance genes and establish their relationships. These focus areas of agricultural bioinformatics are beneficial for crop improvement. In several areas of agriculture, bioinformatics can be used, such as plant pathology, improvement of nutritional quality, development of drought-resistant varieties, and so on. This chapter describes the contribution of bioinformatics to studying the genomic data in plant pathology and their implications for crop improvement and the breeding process. The role of databases and software tools in the area has been highlighted. Finally, the challenges associated with the bioinformatics methods in plant pathology research with their limitations have been discussed.