This chapter explores bioprospecting as a key strategy for identifying biocontrol agents that can help mitigate plant diseases caused by climate change. This phenomenon, intensified by human activities, has created conditions conducive to the proliferation of phytopathogens, thereby posing a serious threat to global food security. Factors, such as increased atmospheric carbon levels, extreme temperature fluctuations, water stress, and the spread of weeds and insect vectors, further intensify this challenge. Bioprospecting is crucial for discovering microorganisms that can serve as natural biocontrol agents and play a vital role in protecting plants through mechanisms such as the production of antagonistic compounds, predation, and the induction of resistance. These microbial interactions not only control pathogens but also support plant growth and health in increasingly challenging environments. This chapter emphasizes the importance of integrating advanced omics techniques to enhance our understanding of microorganism-plant interactions, which would allow for the development of more effective and targeted bioinoculants. It also highlights the need to transfer these technologies to agricultural systems with precision and at scale, reduce reliance on chemical pesticides, and promote more sustainable farming practices. In this context, bioprospecting for phytopathogen control has emerged as a promising solution, poised to contribute to a more resilient and sustainable agricultural future in the face of climate change while also aligning with the principles of organic farming.