In marine industries, severe economic losses are caused by accumulating organisms on surfaces in biofouling processes. Establishing a universal and nontoxic protocol to eliminate biofouling has been a notoriously difficult task due to the complexity of the marine organisms' interactions with surfaces and the chemical, mechanical, and morphological diversity of the surfaces involved. The tremendous variety of environmental parameters in marine environments further complicates this field. For efficient surface engineering to combat fouling, secretion, chemical structure, and properties of biobased adhesives and adhesion mechanisms must be understood. Advanced characterization techniques, like Atomic Force Microscopy (AFM), now allow one to study the three parameters determining surface adhesion and, eventually, fouling, i.e., morphology, chemistry, and surface mechanical modulus. By AFM, characterization can now be performed across length scales from nanometers to hundreds of micrometers. This review provides an up-to-date account of the most promising AFM-based approaches for imaging and characterizing natural adhesives provided by marine organisms. We summarize the current understanding of the molecular basis and the related relevant processes of marine fouling. We focus on applications of AFM "beyond imaging", i.e., to study interactions between adhesives and the surfaces involved. Additionally, we discuss the performance enhancement of polymer antifouling coatings using information derived from AFM. Knowledge and control of marine adhesion can be applied to prevent marine fouling, as well as to design bioadhesives to enhance potential medical applications. We present some milestone results and conclude with an outlook discussing novel possibilities for designing antifouling coatings and medical bioadhesives.