The use of synthetic fungicides to control fungal diseases has growing limitations due to eco-toxicological risks. Therefore, it is necessary to replace or integrate high risk chemicals with safer tools for human health and environment. Consequently, research on the selection, evaluation, characterization, and use of biocontrol agents (BCAs) has consistently increased in the last decades. BCA formulates, particularly in some countries, are still scarce in coping with the growing demand for their use in sustainable agricultural management. To foster development and utilization of new effective bioformulates, there is a need to optimize BCA activity, to share knowledge on their formulation processes and to simplify the registration procedures. Studies based on new molecular tools can significantly contribute to achieve such objectives. The present review provides the state of the art on biocontrol of fungal plant diseases with special emphasis on (i) features of the most studied BCAs; (ii) key strategies to optimize selection and use of BCAs (iii); mechanisms of action of the main BCAs; (iv) molecular tools and metagenomic studies in the selection and use of BCAs; (v) main issues and constraints in the registration and commercialization of BCAs, and (vi) perspectives in the biocontrol of fungal plant diseases.