Single crystals of self-synthesized mordenite−Na were used for incorporation of the cationic dye molecule thionin blue (C12H10N3S+). The planar organic molecule (7.5 × 15 Å), which fits into the large 12-membered ring channel of mordenite, was incorporated by ion-exchange replacing extraframework Na+ cations. Deep blue thionin-exchanged mordenite crystals were chemically analyzed by electron microprobe yielding the composition Na5.5Thionin0.4Si42.02Al5.88O96 × nH2O indicating that the large 12-membered ring channels of mordenite are less than half-filled by dye molecules. X-ray data collection of thionin-loaded mordenite single crystals was performed at 120 K with synchrotron radiation (λ = 0.80000 Å) using the single-crystal diffraction line at the Swiss Norwegian Beamline, SNBL (ESRF, Grenoble) where diffracted intensities were registered with an MAR image plate. The structure of thionin−mordenite−Na was refined in the monoclinic space group Cc converging at R1 = 5.53%. Optical microscopy of dye-loaded mordenite single crystals using plane-polarized light showed striking pleochroism due to anisotropic light absorption caused by the preferred orientation of the molecule's transition-dipole moment. Corresponding anisotropic phenomena were also observed by fluorescence microscopy. Four low populated thionin sites were located in the large mordenite channel. Determined S···O (2.97(1)−3.18(1) Å), C···O (3.11(1)−3.36(2) Å) and N···O (3.04(1)−3.20(1) Å) distances from the dye molecule to the channel wall indicate electrostatic interaction with the framework. The molecules are arranged slightly inclined within the large 12-membered ring channels showing significant occupational disorder along the channel axis. The flat geometry of the thionin molecule enables a rotation of about 12° in each direction causing distinct disorder within the channel cross section.