The structure of zeolite SSZ-43 was determined by 3D electron diffraction, synchrotron X-ray powder diffraction, and high-resolution transmission electron microscopy. The SSZ-43 framework forms one-dimensional, sinusoidal 12-ring channels from 5 4 6 1 butterfly units commonly found in other zeolites, but with unique 6.5 × 6.5 Å apertures and 12-ring 6.5 × 8.9 Å windows perpendicular to the channels. SSZ-43 crystals are intergrowths of two polytypes: ~90% orthorhombic polytype A with ABAB stacking of the 12-rings, and ~10% monoclinic polytype B with ABCABC stacking. Molecular modeling performed on the idealized Si-SSZ-43 structure along with empirical relationships for zeolite selectivity in boron-and aluminumcontaining synthesis gels were used in a combined approach to design new di-quaternary ammonium organic structure-directing agents (OSDAs). Experimental trials demonstrated that the new OSDAs produced SSZ-43 over a broader range of compositions than previous mono-quaternary OSDAs.