The atomic force microscope (AFM) allows visualization of the assembly and molecular interactions of single proteins. Most recently, AFM images of bacterial membranes have revealed details of the supramolecular architecture of bacterial photosynthetic apparatus in different species. The near-native experimental conditions used in AFM imaging reduce artefacts and make AFM ideal for studying native conformations. High-resolution AFM of native membranes has revealed variation in core-complex architectures amongst species.