Crop protection is pivotal to maintain abundant production of high quality. Over the past 100 years, use of chemical fertilizers and pathocides and good agronomical practices enabled growers to maintain improved crop productivity. However, extensive use of chemicals during the last few decades in controlling pests and diseases resulted in negative impacts on the environment, producing inferior quality and harming consumer health. In recent times, diverse approaches are being used to manage and/or mitigate a variety of pathogens for control of plant diseases. Biological control is the alternative approach for disease management that is eco-friendly and reduces the amount of human contact with harmful chemicals and their residues. A variety of biocontrol agents including fungi and bacteria have been identified but require effective adoption and further development of such agents. This requires a better understanding of the intricate interactions among the pathogen, plants and environment towards sustainable agriculture. Beyond the field assessment, the analysis of microbial communities with culture-independent molecular techniques including sequencing technologies and genomics information has begun a new era of plant disease management. Keywords Biocontrol agent • Plant-pathogen interaction • Eco-friendly plant disease management • Sustainable agriculture • Socioeconomic impact 8.1 Introduction During the last 40 years, the world population has increased by 90%, while food production has increased only by 25% per head. It is estimated that 39% more production is needed worldwide to feed an additional 1.5 billion mouths by 2020