In a process of bioleaching of sulfides, the surface of target mineral is sometimes covered with intermediates and final products to interfere the extraction of metal. Understanding characterization and formation order of secondary minerals, which are responsible for passivation, is a key to resolve the passivation. In the present article, identification of secondary minerals and intermediates in a process of bioleaching of several sulfides by X-ray photoelectron spectroscopy, Raman spectroscopy, identification of jarosite group minerals using Raman spectroscopy, and expectation of formation order of secondary minerals by SEM-EDX and TEM observation are overviewed. Direct observation of a nanodomain by TEM provided a useful information on amorphous secondary minerals. In bioleaching of arsenic-bearing copper sulfides, which are expected to be a new target in the near future, a passivation model was proposed to keep maximizing Cu recovery and minimizing As solubilization, based on combination of solid characterization with aqueous observation.