Extended X-ray absorption (EXAFS) measurements of iron-substituted bacteriorhodopsin revealed for the light-adapted state (bRLA) a homogeneous distribution of the first-shell ligands of iron. In Contrary to this result, the dark-adapted (bRDA) and the M-state (bRM) display significant heterogeneity at the iron site with bRDA intermediate between bRM and bRLA in average distance. These data provide direct evidence of structural changes at the membrane associated with photocycle changes at the cation-binding site.