Parageneses and chemical compositions of secondary minerals in many core samples of the Onikobe geothermal system, Japan, were investigated in detail in order to evaluate the controls of geothermal waters on alterations of andesitic-dacitic rocks. Depth zonations of secondary minerals were delineated for Cazeolites as mordenite → laumontite → yugawaralite → wairakite and clay minerals as smectite (± alkaline smectite) → chlorite/smectite → chlorite. Compositional variations with depth (hence temperature) are apparent for smectite/chlorite and illite/chlorite interstratified clay minerals but not for wairakite. Both prehnite and epidote at depth have Fe-rich compositions and become more aluminous with increasing depth. The ubiquitous occurrence of pyrite and rare magnetite and the absence of hematite suggest that the Onikobe system had f S 2 - f O 2 conditions within the pyrite stability field. The occurrence of abundant calcite and Ca-zeolites indicates that thermal waters at depth are neutral to slightly alkaline and X CO 2 is very low to stabilize CaAl-silicates. This conclusion is consistent with the production of a remarkable amount of alkaline high-temperature steam and thermal waters in a newly drilled production well.