A method of fabricating an electrophoretic display device includes forming a gate electrode, a gate line, a data line and a thin film transistor on a substrate having a display region, a non-display region at a periphery of the display region and a cut portion at an outer region of the non-display region; forming a passivation layer over the thin film transistor; forming a pixel electrode connected to the thin film transistor; forming an align mark in the cut portion; attaching an electrophoresis film onto the pixel electrode; forming a color filter layer on the base film using the align mark; wherein the step of forming the align mark is simultaneously performed with one of the step of forming the gate line, the step of forming the data line, and the step of forming the pixel electrode.