Here we present a scanning probe microscopy method that allows for the identification of regions of different polarity (i.e. hydrophilicity) in thin organic films. This technique is based on the analysis of the difference between phase images generated at different applied bias voltages in tapping-mode atomic force microscopy. We show that, without any chemical modification of the microscope tip, it is possible to investigate surface properties of complex macromolecular layers, yielding new insight into the functional properties of the photosynthetic electron transport macromolecular complex, Photosystem I.