Hybrid thin films containing N,N'-bis(2-phosphonoethyl)-1,4,5,8-naphthalenediimide (PNDI) and zinc cations (PNDI/Zn films) were built on silicon and indium tin oxide (ITO) substrates by a simple layer-by-layer deposition process. Silicon substrates primed with a layer of phosphonate groups were immersed alternately into zinc nitrate and PNDI aqueous solutions, yielding PNDI/Zn films containing up to 40 layers. ITO substrates, on the other hand, were used without priming, and the deposition sequence began with a PNDI layer. All film growth steps were conducted at room temperature, using aqueous solutions, thus assuring an environmentally clean process. The PNDI/Zn films were studied by X-ray reflectivity and grazing angle X-ray diffraction, using synchrotron radiation source. The films were constituted by crystallites, containing zinc phosphonate layers oriented nearly parallel to the substrate. PNDI/Zn films on ITO were reduced to stable free radicals, which were observed by UV-visible spectroscopy. Moreover, PNDI/Zn bulk materials with structural analogy with the films were produced.