A facultative dissimilatory metal-reducing bacterium, Shewanella sp. strain HN-41, was used to produce magnetite nanoparticles from a precursor, poorly crystalline iron-oxyhydroxide akaganeite ($eta$-FeOOH), by reducing Fe(III). The diameter of the biogenic magnetite nanoparticles ranged from 26 nm to 38 nm, characterized by dynamic light scattering spectrophotometry. The magnetite nanoparticles consisted of mostly uniformly shaped spheres, which were identified by electron microscopy. The magnetometry revealed the superparamagnetic property of the magnetic nanoparticles. The atomic structure of the biogenic magnetite, which was determined by extended X-ray absorption fine structure spectroscopic analysis, showed similar atomic structural parameters, such as atomic distances and coordinations, to typical magnetite mineral.