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 x 15 Angstrom), 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 Na(5.5)Thionin(0.4)Si(42.02)Al(5.88)O(96) x nH(2)O 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 ( lambda = 0.80000 Angstrom) 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 RI = 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) Angstrom), C...O (3.11(1)-3.36(2) Angstrom) and N...O (3.04(1)-3.20(1) Angstrom) 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 12degrees in each direction causing distinct disorder within the channel cross section.