The methylene blue (MB) sensitized photooxidations of anthracene (AN), 9,10-diphenyl-anthracene (DPA) and 2-dimethylaminoanthracene (DMA) have been studied in ethanol and in Nafion, a perfluorinated polymer with sulfonate groups. Spectroscopic studies indicate that the incorporated chromophores are heterogeneously distributed in the micelle-like polymer. The uncharged aromatic hydrocarbons are located in the non-polar polymer backbone region while the positively charged species reside at the interface of aqueous cluster regions in the membrane. The MB-sensitized photooxidations of all anthracenes are faster in Nafion than in ethanol. Furthermore the photooxidation of AN is 1.6 times higher in D2O-swollen Nafion than in H2O-swollen samples. Analysis of the photodegradation data suggests that these results can be attributed to the heterogeneous siting of the chemical species and the behaviour of singlet oxygen in the membrane.