Magnetotactic bacteria guide themselves to optimal growth environments by a process termed magneto-aerotaxis, in which chains of intracellular magnetic nanoparticles, known as magnetosomes, orient along the Earth's geomagnetic field lines as a guide to efficiently locate oxygen-poor regions. From an external standpoint, this unique magnetotactic navigation system is regulated by key components: a magnetic nano-compass (magnetosome chain), a propulsion system (flagellar motility), and some magnetically-activated sensor (signal transduction). We hope to gain insight into these external systems by deconstructing the internal regulation of magnetotactic navigation from a genetics perspective. While genomic regions have been identified that encode magnetosome-related genes, little is known about how these genes regulate magnetosome production and how they interact with flagellar and cytoskeletal components to achieve guided motility. Here, we explore the genetic response of Magnetospirillum magneticum strain AMB-1 to an applied electromagnetic field as a means to identify genes activated by magnetic stimulation, focusing on magnetosome island, magnetotactic islet, flagellar, and cytoskeleton genes. AMB-1 cultures were subjected to static, high magnetic field (10G) generated by a solenoid or to low frequency pulsed magnetic field (between 0G and 10G at 0.0033 Hz) for 30 min, 1 hour, 3 hours or 6 hours. After extracting total RNA and converting to cDNA, quantitative real time-PCR was performed to measure relative transcription levels. Both static and pulsed magnetic fields altered gene expression with the greatest changes occurring at shorter time points. Differential regulation of mamK and mamK-like genes responsible for mechanical stabilization of magnetosomes, in addition to flagellar anchor protein fliF and actin-like structural protein mreB, provides evidence for altered regulation of mechanics- and motility-related processes with magnetic activation. We believe these findings provide significant targets for understanding the genetic regulation and mechanics of magnetically-driven bionavigation.