We observe for the first time a structural phase transition in the oxyborate Fe3O2BO3 which occurs along three leg ladders present in this material. X-ray diffraction shows that this transition at 283 K is associated with a new phase where atomic displacements occur in alternate directions perpendicular to the axis and within the plane of the ladders. Magnetic data show that these displacements lead to the formation of singlet pairs which dissociate close to the structural transition. Anomalies in the transport properties also occur close to 283 K showing that the structural transition is related to a charge ordering phenomenon in a low dimensional structure.