Four dyes (2-DASPI, 4-DASPI, LDS698, and LDS722) derived from the stilbazolium skeleton have been intercalated into optically transparent Na-fluorine mica layers. X-ray diffraction data show that the long axis of DASPI dyes is aligned parallel to the layer, largely maintaining their solution phase structure. On the other hand, conformation of LS dyes appears to be significantly distorted, due to the two-dimensional confinement. A huge difference in the fluorescence lifetimes between DASPI and LDS dyes in mica was described by the chromophore molecular structures.