Spring water at Masutomi mineral springs，Yamanashi Prefecture contains abundant arsenic（As）and radon（Rn）．Reddish brown，green，and white microbial mats（biomats）can be seen in the mineral springs．The biomats were observed by opticai microscope，fluorescence microscope（DAPI dying），SEM and TEM．ED-XRF，XRD and SEM-EDX were used for chemical and mineralogical examination．Reddish brown biomats are composed of Fe，Si，and As．Green and white biomats consist of calcite．In the reddish brown biomats，bacteria accumulate Fe，Si and As form biominerals around the cell wall．White biomats contain little As，but that present is concentrated in thin layered structures in hardened biomats．This study indicated that bacteria in reddish brown biomats accumulate Fe，Si，As and Ra to form non-toxic type As and Rn in Masutomi mineral spring water．