Applications of atomic force microscopy (AFM) to imaging of DNA with various structures, topologies, and complexes with proteins are reviewed. The emphasis is given to methods utilizing chemical functionalization of mica, enabling AFM visualization of different DNA structures. Special attention is given to the ability of AFM to image the dynamics of DNA at the nanoscale. The capabilities of time‐lapse AFM in aqueous solutions are illustrated by imaging of dynamic processes as transitions of local alternative structures (transition of DNA between H and B forms). The application of AFM to studies of protein–DNA complexes is illustrated by a few examples of imaging site‐specific complexes, as well as systems such as chromatin. The time‐lapse AFM studies of protein–DNA complexes including very recent advances with the use of high‐speed AFM are reviewed.