Molecular electronics aims at exploiting the internal structure and electronic orbitals of molecules to construct functional building blocks1. To date, however, the overwhelming majority of experimentally realized single-molecule junctions can be described as single quantum dots, where transport is mainly determined by the alignment of the molecular orbital levels with respect to the Fermi energies of the electrodes2 and the electronic coupling with those electrodes3,4. Particularly appealing exceptions include molecules in which two moieties are twisted with respect to each other5,6 and molecules in which quantum interference effects are possible7,8. Here, we report the experimental observation of pronounced negative differential conductance in the current–voltage characteristics of a single molecule in break junctions. The molecule of interest consists of two conjugated arms, connected by a non-conjugated segment, resulting in two coupled sites. A voltage applied across the molecule pulls the energy of the sites apart, suppressing resonant transport through the molecule and causing the current to decrease. A generic theoretical model based on a two-site molecular orbital structure captures the experimental findings well, as confirmed by density functional theory with non-equilibrium Green’s functions calculations that include the effect of the bias. Our results point towards a conductance mechanism mediated by the intrinsic molecular orbitals alignment of the molecule.