The growing antimicrobial resistance and persistence of pathogenic microorganisms in infections–particularly in nosocomial infections–have become a major problem for public health worldwide. One of the main causes of these issues is the formation of biofilms, which are microbial communities associated with extracellular polymeric substances (EPS) that form a slimy extracellular matrix, causing the bacteria to become more tolerant to usual drugs in these structures. Thus, the search for new antibiofilm compounds is part of a strategy to deal with this problem. Endophytic microorganisms such as bacteria and fungi, mutualistically associated with plants, are sources of compounds with biological properties, including antimicrobials, and can be important allies in the synthesis of antibiofilm. These secondary metabolites can interfere with cell-to-cell communication and cell adhesion ability, promoting the dispersal of bacterial colonies and affecting biofilm. Since endophytes are cultivable in laboratory conditions, these microorganisms are environmentally friendly, as they do not contribute to pollution, are easy to handle and are produced on a large scale. Furthermore, metabolites from endophytes are of natural origin and may contribute to the reduced use of synthetic drugs. Considering these aspects, this chapter will focus on the characterization of endophytic microorganisms as potential active sources of antibiofilm and antimicrobial compounds with applications in medicine.