Metastable phase, which has a lager value of Gibbs free energy than that of the stable phase, commonly occurs in nature against the thermodynamic regulation. Microtexture and microstructure of some metastable-phase minerals (opal-CT, marcasite and wurtzite) are studied by high-resolution transmission electron microscopy. Disordered stacking structures are commonly observed in the metastable phases. In the case of the opal-CT (Hosaka and Akase opal mines, Japan) and marcasite (Ikezuki, Japan), highly ordered domains appear around the domains with disordered stacking structure. Chocaya-Animas wurtzite crystals overgrow on the domains of disordered stackings of sphalerite and wurtzite, which were formed from ordered sphalerite.