Records of natural remanent magnetization (NRM) and geomagnetic polarity reversals preserved within ferromanganese (Fe-Mn) crusts, together with the application of fine-resolution magnetostratigraphic analysis, have been successfully demonstrated. However, because Fe-bearing precipitates or minerals are thought to be either oxides and/or hydroxides precipitated from ambient oxic seawater or detrital minerals, the magnetic properties of the ferromagnetic minerals and the genetic mechanisms remain controversial; moreover, the origin of the NRM is unclear. Here, we show that nanometer-scale magnetite crystals found in Fe-Mn crusts from the Pacific Ocean and South China Sea are magnetosome fossils based on their narrow size range, chain arrangement, chemical purity, and crystallographic perfection, as indicated by transmission electron microscopy. Furthermore, our new data from rock magnetic and electron paramagnetic resonance analyses, combined with a previously reported micro-magnetostratigraphic sequence, indicate that magnetotactic bacteria and their post-mortem remains contribute to a biogeochemical remanent magnetization of Fe-Mn crusts. In addition, the results provide evidence for a previously unappreciated pathway for the biogeochemical cycling of iron in the deep ocean.