Minerals are multi-component systems in which the solid phase is polycrystalline and sometimes polyamorphous. Although there are many methods to characterize the major components and crystalline matter to an adequate extent, often it is difficult to get a complete picture with fine-grained or amorphous samples. In this research, we studied mineral samples rich in jarosite and muscovite using X-ray diffraction and spectroscopy techniques to identify both crystalline and amorphous content of the mineral sample. Minerals were fractionated to different particles size based on Stokes' law settling. Powder X-ray diffraction was then used to study the whole rock and different fractions. Siroquant software was used to determine the percentage ratios of different minerals present in the whole rock sample and different fractions. Diffuse reflectance spectroscopy was used to analyze both crystalline and amorphous fractions of mineral sample. Using diffuse reflectance spectroscopy, it was possible to identify different silica forms (quartz, cristobalite and tridymite) but the same was not possible with different jarosite species (hydronium jarosite, ammoniojarosite, natrojarosite argentojarosite and plumbojarosite). Subtraction of spectra to identify individual mineral species is discussed. Results are also discussed on development of methods to identify jarosite species using Raman spectroscopy.