Scanning tunneling microscopy (STM) of the Si(111)-7 × 7 reconstructed surface at 5 K reveals that the highly symmetric STM image found at room temperature does not reflect the lowest energy, ground state of this system. Instead, the ground state has certain adatom charge densities distorted by ≈0.2–0.4 Å from the symmetric STM charge density positions observed at 300 K. This agrees with adatom ion core displacements in both a Patterson map and two additional phase-reconstructed atom maps. Such ion core distortions are consistent with the Jahn–Teller effect associated with the threefold mirror symmetry of the Si(111)-7 × 7 and its antiphase, faulted structure. The nodal properties of the electronic states of an underlying 7 × 7 honeycomb that arise from threefold symmetry are determined from solutions of the 2D inhomogeneous Helmholtz equation, and provide insight to the observed temperature-dependent charge density changes. It is shown that an excited state of the honeycomb cells of a Si(111)-7 × 7 support the higher symmetry charge densities observed at room temperature and the presence of strong electron–phonon coupling. The role of symmetry and anharmonicity in defining the structure and electronic interactions in the Si(111)-7 × 7 are discussed.