Magnetic separation of target cells from mixtures, such as peripheral blood and bone marrow, has considerable practical potential in research and medical applications. Among the current cell separation techniques, magnetic cell separation using immunomagnetic particles has been routinely applied and has proven rapidness and simplicity. Magnetospirillum magneticum AMB-1 synthesizes intracellular nano-sized bacterial magnetic particles (BacMPs) that are individually enveloped by a stable lipid bilayer membrane. BacMPs, which exhibit strong ferrimagnetism, can be collected easily with commercially available permanent magnets. In this study, a novel magnetic nanoparticle displaying protein G (protein G-BacMPs) was fabricated, and one-step cell separation for direct cell separation from whole blood was performed using the protein G-BacMPs. B lymphocytes (CD20+ cells), which cover less than 0.3×10−2 % of whole blood cells, were separated with 93% purity using protein G-BacMPs binding with anti-CD20 monoclonal antibodies. The results of this study demonstrate the utility of protein G-BacMPs and the magnetic cell separation approach based on protein G-BacMPs in numerous applications.