Off-axis electron holography in the transmission electron microscope was used to correlate the physical and magnetic microstructure of magnetite nanocrystals in magnetotactic bacteria. The magnetite crystals were all single magnetic domains, and the magnetization directions of small superparamagnetic crystals were constrained by magnetic interactions with larger crystals in the chains. Shape anisotropy was found to dominate magnetocrystalline anisotropy in elongated crystals. A coercive field between 300 and 450 oersted was determined for one chain.