Seismic tomographic images indicate that subducted lithosphere is transported into the deep mantle1. Petrologic modelling shows that water contained in subducted slabs can be carried to depths of at least 200 km (ref. 2); however, whether the hydrated slab signature is preserved at greater depths depends on diffusion rates. Experimental studies give conflicting results on the question of hydrogen preservation. On a small scale, hydrogen equilibration with ambient mantle should be rapid3, 4, implying that the slab hydrogen signature may not be preserved in the deep mantle5. However, on large scales the time required for diffusive equilibration is longer and hydrogen anomalies may persist6, 7. Here we present hydrogen and boron data from submarine volcanic glasses erupted in the Manus back-arc basin, southwestern Pacific Ocean. We find that samples with low hydrogen-isotope values also exhibit the geochemical signature of dehydrated, subducted lithosphere. Combined with additional geochemical and geophysical data, we interpret this as direct evidence for the preservation of hydrogen anomalies in an ancient slab in the mantle. Our geochemical data are consistent with experimental estimates of diffusion for the upper mantle6 and transition zone7. We conclude that hydrogen anomalies can persist in the mantle without suffering complete diffusive equilibration over timescales of up to a billion years.