Because of the rapid increase in microbial resistance to existing antimicrobial agents, there is a need to explore unique sources of antibiotics from nature. Hence, current scientific endeavors have focused on the bioprospecting of secondary metabolites found among microbes, with the special aim of finding naturally occurring compounds possessing antibacterial qualities that originate from endosymbionts. All plant species, regardless of their type, are believed to harbor endosymbiotic microorganisms. In addition to the benefits, they confer to the host plants, i.e., fungal endosymbionts produce a wide range of natural chemicals for exploitation with possible utilization in the fields of medicine, agriculture, and pharmaceuticals. The procedures described in the current protocols focus on examining the antibacterial properties of fungal endosymbionts isolated in higher plants.