The widespread magnetotactic bacteria have the peculiar capacity of navigation along the geomagnetic field. Despite their ubiquitous distribution, only few axenic cultures have been obtained worldwide. In this study, we reported the first axenic culture of magnetotactic bacteria isolated from the Mediterranean Sea. This magneto-ovoid strain MO-1 grew in chemically defined O2 gradient minimal media at the oxic–anoxic transition zone. It is phylogenetically related to Magnetococcus sp. MC-1 but might represent a novel genus of Proteobacteria. Pulsed-field gel electrophoresis analysis indicated that the genome size of the MO-1 strain is 5 ± 0.5 Mb, with four rRNA operons. Each cell synthesizes about 17 magnetosomes within a single chain, two phosphorous-oxygen-rich globules and one to seven lipid storage granules. The magnetosomes chain seems to divide in the centre during cell division giving rise to two daughter cells with an approximately equal number of magnetosomes. The MO-1 cell possesses two bundles of seven individual flagella that were enveloped in a unique sheath. They swam towards the north pole with a velocity up to 300 μm per second with frequent change from right-hand to left-hand helical trajectory. Using a magneto-spectrophotometry assay we showed that MO-1 flagella were powered by both proton-motive force and sodium ion gradient, which is a rare feature among bacteria.