A new ordering scheme in cationic-deficient perovskite-like phases of the Ban(Mo,Nb)n-δO3n-x system has been described for the composition Ba3MoNbO8.5, which has an oxygen stoichiometry between those of the 9R polytype and the palmierite structure. An electron diffraction and high-resolution electron microscopy study shows that the oxygen defect with respect to the 9R polytype (hhc)3 leads to an ordered distribution of octahedra and tetrahedra in a 3:2 ratio in the cubic layers. The flexibility of the (hhc)3 stacking sequence allows the formation of a modulated structure through an ordered shearing mechanism along c by introducing mixed BaO2.6 cubic layers in the 9R polytype.