In a recent study, we demonstrated that in the plasma membrane AQP4 is organized into several distinct large multisubunit complexes. In this study, we analysed whether these pools are similarly affected in dystrophin-deficient mice and immunolocalized the sites of dystrophin-dependent and -independent AQP4 pools. Western blot performed on two-dimensional Blue Native/SDS-PAGE membranes indicated that, among the AQP4 pools, it was mainly a large multisubunit complex that was specifically affected in dystrophin-deficient mice (DP71 and mdx3cv mice). This dystrophin-dependent AQP4 pool was immunolocalized in perivascular astrocytes, since it was found to be significantly altered in both types of dystrophin-deficient mice. Dystrophin-independent pools were immunolocalized in the granular cell layer of the cerebellum and in the subpial endfoot layer and ependymal cells in the brain. These data provide a better understanding on the association between AQP4 and the dystrophin-glycoprotein complex in the central nervous system.