We report here results from a deep‐sea magnetic survey using an autonomous underwater vehicle over the Hakurei hydrothermal site, in the middle Okinawa Trough. Magnetic inversion revealed that the Hakurei site is associated with well‐defined high‐magnetization zones distributed within a broad low‐magnetization zone. Results from rock magnetic measurements, performed on sulfide ore samples obtained by drilling, showed that some samples possessed extremely high natural remanent magnetization (NRM) (as much as 6.8–953.0 A/m), although most of the measured samples had much lower NRM. These high‐NRM samples were characterized by high Königsberger ratios (101−103), indicating much larger NRM than induced magnetization, and contained pyrrhotite as the only magnetic mineral. This suggests that NRM carried by pyrrhotite is the source of the observed magnetic anomalies. The wide range of NRM intensity was considered to be due to a highly heterogeneous distribution of pyrrhotite, because pyrrhotite was commonly identified in both the high‐NRM and low‐NRM samples. Pyrrhotite production may have been occasionally drastically increased, with highly magnetic ores formed as a result. Rapid burial of active vents may result in the creation of an extensive reducing environment under the seafloor, which is favorable to pyrrhotite production, and may also prevent oxidation of pyrrhotite by isolating it from seawater. Because the magnetization intensity of sulfide ores was highly variable, it would not be straightforward to estimate the quantity of ore deposits from the magnetic anomalies. Nevertheless, this study demonstrates the usefulness of magnetic surveys in detecting hydrothermal deposits.