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In this paper, we use a Rao-Blackwellized Particle Filter (RBPF) for GNSS localization subject to ionospheric scintillation. The proposed filter assumes a mixed state vector containing continuous state variables related to the tridimensional (3D) aircraft position and GNSS receiver bias/drift, and a discrete scintillation switching variable for each satellite in view that indicates the presence or absence of scintillation. The dynamics of the scintillation switching variable is modeled by a Markov Chain with known a priori transition probabilities. The variance of the GNSS pseudorange measurement noise changes then as a function of the scintillation variable. Simulation results show that the proposed RBPF achieves a reduced root mean-square 3D position estimation error that is below the corresponding errors for the optimistic and the pessimistic Extended Kalman Filters, which assume, respectively, absence and presence of scintillation at all time instants.