Bacterial biomineralization of clay minerals was studied by SEM-EDX and TEM. Two kinds of samples obtained from Kutani glaze and the deep sea sediment of Iheya Basin, Okinawa Trough. Halloysite particles were observed on the cell wall of cyanobacteria in the Kutani glaze solution. Halloysite was introduced from feldspar in the processes of biomineralization by cyanobacteria. On the other hand, iron rich nontronite was formed with bacterial extraction of Mg and Al ions in the deep sea sediments, Iheya Basin. These results indicate that the formation of clay minerals depends on not only physical precipitation but also the processes of bacterial biomineralization associated with extraction of specific elements.