Fungal infections that attack plants cause the vast majority of illnesses encountered in agricultural and horticultural environments. These phytopathogens have evolved strategies for invading plants, obtaining nutrients, and for its growth and development. The biological control of plant pathogens refers to the reduction of disease-causing agents by microorganisms and their products. Endophytes are plant-associated microorganisms that may survive within plant tissues without infecting or harming the host plant. Many endophytes may produce a wide range of active metabolites, which can be used directly or indirectly in a number of therapeutic applications. Secondary compounds are frequently used as chemical defenses against microbes, insects, higher predators, and even other plants, as pollinator attractants, or as chemical responses to environmental challenges. Secondary metabolites (SM) are often higher-value, lower-volume products than primary metabolites, which are employed commercially as physiologically active substances and are generated in specific cell types and at discrete developmental phases. Fungi inhibited by VOCs and SMs generated by Cupressaceae endophytes that includes Diplodia seriata, Spencermartinsia viticola, Pyricularia oryzae, and Phaeobotryon cupressi. Alternaria, Aspergillus, Penicillia, and Trichoderma. Acids, alcohols, esters, lipids, and ketones are among the five types of chemicals identified in these endophytes. Antimicrobial metabolites are low-molecular-weight chemicals that are effective at low dosages against pathogenic microbes. Antibiosis is vital in the biocontrol of plant disease, and it is frequently supplemented by competition and parasitism. Trichoderma is an excellent example of a biocontrol agent that generates a variety of secondary metabolites, including butenolides, gliotoxin, gliovirin, pyrones, and volatile terpenes.