Hydrogen in the Earth's deep interior has been thought to exist as a hydroxyl group in high-pressure minerals. We present Muon Spin Rotation experiments on SiO2 stishovite, which is an archetypal high-pressure mineral. Positive muon (which can be considered as a light isotope of proton) implanted in stishovite was found to capture electron to form muonium (corresponding to neutral hydrogen). The hyperfine-coupling parameter and the relaxation rate of spin polarization of muonium in stishovite were measured to be very large, suggesting that muonium is squeezed in small and anisotropic interstitial voids without binding to silicon or oxygen. These results imply that hydrogen may also exist in the form of neutral atomic hydrogen in the deep mantle.