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A novel perfluorinated magnesium phthalocyanine (MgPcF64) was synthesized and employed to probe nanodomains in hydrophobically modified, amphiphilic cationic polyelectrolytes bearing alkyl and/or fluoroalkyl side chains. MgPcF64 was found to be solubilized exclusively in the aqueous solutions of the fluorocarbon modified polycations, occupying the perfluorinated nanocompartments provided, while analogous polyelectrolytes with alkyl side chains forming hydrocarbon nanocompartments could not host the MgPcF64 dye. Multilayer films were fabricated by means of the layer-by-layer (LbL) deposition method using sodium poly(styrene sulfonate) as a polyanion. Linear multilayer growth was confirmed by UV-Vis spectroscopy and spectroscopic ellipsometry. Atomic force microscopy studies indicated that the micellar conformation of the polycations is preserved in the multilayer films. Fluorescence spectroscopy measurements confirmed that MgPcF64 stays embedded inside the fluorocarbon domains after the deposition process. This facile way of selectively incorporating water-insoluble, photoactive molecules into the structure of polyelectrolyte multilayers may be utilized for nanoengineering of ultrathin film-based optoelectronic devices.