Herein, we synthesise various polymorphs of MnO2 through hydrothermal technique. Formation of pure tetragonal structured alpha-, beta- and mixture of alpha and beta phase of MnO2 are identified through Fourier transform infrared spectroscopy (FTIR) and X-Ray diffraction (XRD).Rietveld refinement reviles 73% of alpha-MnO2 and 27% of beta-MnO2 present in alpha beta-MnO2. From Field emission scanning electron micrographs (FESEM), average diameter of alpha- and beta-MnO2 nanorods is found to be 36 nm and 23 nm, respectively, while in alpha beta-MnO2, nanorods of two different sizes, 28 and 116 nm are observed. Among all polymorphs, small size of nanorods in beta-MnO2 results high specific capacitance. Through UV-visible absorption spectra, the optical band gap of alpha-, beta- and alpha beta-MnO2 nanorods are estimated to be 1.53, 1.30 and 1.45 eV, respectively. XPS confirms the presence of large concentration of Mn3+ in alpha- and alpha beta-MnO2 nanorods results high effective magnetic moment in comparison to the theoretical one which is almost same in beta-MnO2. Henceforth, we evaluate the accurate composition of MnO2 as alpha-MnO1.48, beta-MnO1.86 and alpha beta-MnO1.15. Spin-glass/cluster-glass behavior is confirmed from ac susceptibility and remanent magnetization measurements in beta-MnO2 and alpha beta-MnO2 which is absent in alpha-MnO2 depending on a critical concentration of Mn3+ ions.