Although experimental studies have shown dislocation creep to be an important deformation mechanism in magnetite at medium to high temperature, evidence of intracrystalline deformation in magnetite remains to be established in natural tectonically deformed rocks. In this study we investigate intracrystalline deformation features and nanostructures in elongated magnetite from a naturally deformed rock (mylonitized mica schist deformed in a large-scale shear zone of the Seve nappe, Swedish Caledonides). The magnetite grains have very high aspect ratios (up to 10.40) that result in very high degree of magnetic anisotropy in the rock. We show low and high angle grain boundaries (LAGB and HAGB) in magnetite using a combination of electron backscatter diffraction and high-resolution transmission electron microscopy (HRTEM) analysis. HRTEM studies on lamellae excavated perpendicular to the LAGB and HAGB reveal translational and rotational Moiré fringes, respectively. Dislocations, slip bands, stacking faults, twins and recrystallized domains are observed in the vicinity of the grain boundaries, thus providing unequivocal evidence of intracrystalline deformation of magnetite. ... mehrOur study also reveals the presence of biotite inclusions intergrown epitaxially with magnetite that show no evidence of lattice defects, thus suggesting that the intracrystalline deformation of magnetite took place under wet conditions. The movement at the grain boundaries is interpreted as a response to regional tectonics with a top-to-NW transport direction. It is established that at the nanoscale, the LAGB and HAGB were favourably oriented to accommodate strain dominantly by translation and rotation, respectively. Thus, the nanotectonic processes are consistent with the regional tectonic reference frame. The importance of evaluating ductile behaviour of magnetite from deformed polymineralic rocks in petrofabric analysis and modeling the relation between strain and rock magnetic anisotropy is discussed.