One of the striking capability of atomic force microscopy (AFM) is the direct observation of surface atoms and adsorbed molecules on nonconductive materials such as zeolites. The observation can be made under various environments including vacuum, ambient and underwater. We have been successful in observing in situ atomic images of heulandite and stilbite (010) surfaces under aqueous environments, and also molecular images of liquid-phase-adsorbed organics on these surfaces. The unprecedented resolution of the AFM imaging enabled us to determine, for the first time, the positions of framework oxygen and extra-framework cations, and furthermore the array and orientation structures of adsorbed molecules such as pyridine bases. The present paper reviews our recent findings on the structure and energetics of those adsorption systems.