We present a theoretical and experimental investigation of the crystalline structure of N,N′-1H,1H-perfluorobutyl dicyanoperylenecarboxydiimide (PDI-FCN2) that has been deduced combining experimental XRD data, obtained from powders, with global-optimization algorithms which allow to identify Bravais lattice, primitive cell parameters, and space group of the crystal. The XRD spectrum calculated for the proposed crystalline structure very well reproduces the measured XRD data. Our results suggest the triclinic lattice structure of spatial groups \documentclass[12pt]{minimal}\begin{document}$P\overline{1}$\end{document}P1¯ and P1, respectively, for the crystalline PDI-FCN2-1,7 and PDI-FCN2-1,6 isomers. In both cases, the primitive cell contains a single molecule. On the proposed crystalline structures, KS-DFT cell energy calculations, including van der Waals interactions, have been performed to assign the minimum energy geometrical structure and orientation of the molecule inside the corresponding primitive cell. These calculations evidence the molecular packing that characterizes the strong anisotropy of the PDI-FCN2 crystal. Electronic band-structures calculated for both isomers within the Kohn-Sham density-functional theory indicate that the crystalline \documentclass[12pt]{minimal}\begin{document}$P\overline{1}$\end{document}P1¯ structure is an indirect gap semiconductor, while the P1 structure is a direct gap semiconductor. The electronic band structure calculations on the optimized crystal geometries highlight strong anisotropy in the dispersion curves \documentclass[12pt]{minimal}\begin{document}$E(\bf k)$\end{document}E(k), which roots at the molecular packing in the crystal. Finally, the vibrational spectrum of both crystalline isomers has been calculated in the harmonic approximation and the dominant vibrational frequencies have been associated to collective motions of selected atoms in the molecules.