Diatomaceous laminites of the Pleistocene Shiobara Group (caldera fill), located in the volcanic front of the Northeastern Japan Arc, are the profundal facies of palaeo-Shiobara Lake. The laminites are subdivided into five types: clastic (Type A), diatom-preserved (Type B), porcelainised (Type C), double (Type D) and reversal (Type E). These varieties are mostly induced by lithification, due to localised hydrothermal alteration represented as the diatom frustules' transformation from opal-A to opal-CT. Type B laminite alters to Type C, Type D and finally Type E laminite in a progressive order. As alteration proceeds, the rock become more consolidated, and lamina texture changes from porous to massive. Exceptionally, Type A laminite, composed of grey terrigenous lamina, shows almost no changes, because of its poor content of diatom frustules. Type B laminite, composed of porous white diatomaceous lamina and grey terrigenous lamina, is replaced by Type C laminite, composed of tightly packed opal-CT lepispheres. Type D laminite is represented as a set of four laminae; grey, white-1, black, and white-2, in upwardsequence. The black laminae result from additional reprecipitation within the white laminae, and laterally fade. Type E laminite is the last stage of the alteration series of the laminites in Shiobara and consists of thin couplets of grey and black laminae. White laminae completely alter to black laminae. These laminite variations are likely derived from alteration by hydrothermal water associated with the caldera. Whereas Type A and B laminites are widely distributed in the basin, the distribution of Type C is restricted. Type D and E laminites are found only at one quarry which yields exceptionally well preserved megafossils: mice, frogs, a feather, fishes, and insects. We hypothesise that such silica transformation may have contributed to preservation of the megafossils by stabilization of the remains of biota and protection of the remains against dissolution.