Membrane vesicle (MV) is a small spherical particle which is produced by bacteria. Although the importance of examining the properties of individual MVs has been increasing in recent years, only the analysis of physical properties in bulk has been done. In this study, we observed the MVs produced by four bacterial species in PBS using high-speed atomic force microscopy with tapping mode, and clarify the physical property of individual MV from phase image. The phase image showed the diversity of MVs physical property such as elasticity. We developed a method to compare the physical property between different samples from phase images. We compared the physical properties of bacterial MVs and liposomes made from bacterial lipid extract. The all species of MVs showed physical heterogeneous, whereas the liposomes showed physical homogenous. Therefore, the physical property analysis using high-speed AFM revealed that the MVs have physical diversity driven from biological phenomena.