A magnetic separator was used to separate magnetic bacteria based on their magnetotactic characteristics. Acidithiobacillus ferrooxidans, a bacterium that could synthesize intra-cellular nanometer magnetic particles, was investigated as an example. Strong magnetic and weak magnetic cells were separated and collected. On average, the number of the magnetic particles present in the strong magnetic cells is more than that of the weak magnetic cells. Moreover, semisolid-plate magnetophoresis showed that the magnetotaxis of strong magnetic cells was stronger than the weak magnetic cells. These results suggest that the magnetic separator can be used to isolate the magnetic bacteria, which will facilitate the research of magnetic bacteria.