Off-axis electron holography in the transmission electron microscope is used to characterize the magnetic microstructure of magnetotactic bacteria. The practical details of the technique are illustrated through the examination of single cells of strains MV-1 and MS-1, which contain crystals of magnetite (Fe3O4) that are ∼50 nm in size and are arranged in chains. Electron holography allows the magnetic domain structures within the nanocrystals to be visualized directly at close to the nanometer scale. The crystals are shown to be single magnetic domains. The magnetization directions of small crystals that would be superparamagnetic if they were isolated are found to be constrained by magnetic interactions with adjacent, larger crystals in the chains. Magnetization reversal processes are followed in situ, allowing a coercive field of between 30 and 45 mT to be measured for the MV-1 cell. To within experimental error, the remanent magnetizations of the chains are found to be equal to the saturation magnetization of magnetite (0.60T). A new approach is used to determine that the magnetic moments of the chains are 7 and 5×10−16Am2 for the 1600-nm long MV-1 and 1200-nm long MS-1 chains examined, respectively. The degree to which the observed magnetic domain structure is reproducible between successive measurements is also addressed.