To investigate the mechanism of inhibition of silver ions on microorganisms, two strains of bacteria, namely Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus aureus (S. aureus), were treated with AgNO3 and studied using combined electron microscopy and X-ray microanalysis. Similar morphological changes occurred in both E. coli and S. aureus cells after Ag+ treatment. The cytoplasm membrane detached from the cell wall. A remarkable electron-light region appeared in the center of the cells, which contained condensed deoxyribonucleic acid (DNA) molecules. There are many small electron-dense granules either surrounding the cell wall or depositing inside the cells. The existence of elements of silver and sulfur in the electron-dense granules and cytoplasm detected by X-ray microanalysis suggested the antibacterial mechanism of silver: DNA lost its replication ability and the protein became inactivated after Ag+ treatment. The slighter morphological changes of S. aureus compared with E. coli recommended a defense system of S. aureus against the inhibitory effects of Ag+ ions.