The natural hydroniumjarosite sample from Cerros Pintados (Chile) was investigated by electron microprobe, single-crystal X-ray diffraction and vibrational spectroscopy (Infrared and Raman). The chemical composition of studied specimens (wt.%, mean of seven analyses) obtained from electron microprobe (in wt.%): Na2O 1.30, K2O 0.23, CaO 0.04, Fe2O3 50.49, Al2O3 0.37, SiO2 0.33, SO3 33.88, H2O (calculated on the basis of Σ(OH−+H3O+) deduced from the charge balance) 13.32, total 99.98, corresponds to the empirical formula (Na0.20K0.02)Σ0.22(Fe2.95Al0.03)Σ2.98 (OH)6.12[(SO4)1.97(SiO4)0.03]Σ2.00 (calculated on the basis of S + Si = 2 a.p.f.u. (atoms per formula unit)). The studied hydroniumjarosite is trigonal, with space group R3İm, with a = 7.3408(2), c = 17.0451(6) Å and V = 795.46(4) Å3. The refined structure architecture is consistent with known jarosite-series minerals, including synthetic hydroniumjarosite. However, in the current study the presence of H3O+ is well documented in difference Fourier maps, where characteristic positive difference Fourier maxima, with apparent trigonal symmetry, were localized in the vicinity of the O4 atom in the channel-voids of the structure. The structure of natural hydroniumjarosite, including the H atoms, was refined to R1 = 0.0166 for 2113 unique observed reflections, with Iobs>3σ(I). The present structure model, which includes the position of the H atom within the hydronium ion, is discussed with regard to the vibration spectroscopy results and earlier published density-functional theory (DFT) calculations for the alunite-like structure containing H3O+.