Electron paramagnetic resonance‐based inter‐residue distance measurements between site‐directed spin‐labelled sites of sensory rhodopsin II (NpSRII) and its transducer NpHtrII from Natronobacterium pharaonis revealed a 2:2 complex with 2‐fold symmetry. The core of the complex is formed by the four transmembrane helices of a transducer dimer. Upon light excitation, the previously reported flap‐like movement of helix F of NpSRII induces a conformational change in the transmembrane domain of the transducer. The inter‐residue distance changes determined provide strong evidence for a rotary motion of the second transmembrane helix of the transducer. This helix rotation becomes uncoupled from changes in the receptor during the last step of the photocycle.