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Abstract Proton conduction is an important property for fuel cell electrolytes. The search for molecular details on proton transport is an ongoing quest. Here, we show that in hydrated yttrium doped barium zirconate using X-ray and neutron diffraction that protons tend to localize near the dopant yttrium as a conjugated superstructure. The proton jump time measured using quasi-elastic neutron scattering follows the Holstein-Samgin polaron model, revealing that proton hopping is weakly coupled to the high-frequency O-H stretching motion, but strongly coupled to low-frequency lattice phonons. The ratio of the proton polaron effective mass, m * , and the proton mass is m * / m  = 2, when coupled to the Zr-O stretching mode, giving experimental evidence of proton pairing in perovskites, as a result of proton-phonon coupling. Possible pathways of a proton pair are provided through Nudge Elastic Band calculations. The pairing of protons, when jumping, is discussed in context of a cooperative protonic charge transport process.