We investigate the magnetic and transport properties of epitaxial stepped Fe3O4 thin films grown with different thicknesses. Magnetization measurements suggest that the steps induce additional anisotropy, which has an easy axis perpendicular to steps and the hard axis along the steps. Separate local transport measurements, with nano-gap contacts along a single step and perpendicular to a single step, suggest the formation of a high density of anti-phase boundaries (APBs) at the step edges are responsible for the step induced anisotropy. Our local transport measurements also indicate that APBs distort the long range charge-ordering of magnetite. (C) 2014 AIP Publishing LLC.