Electrophoresis device including: a first flow passage extending in a first direction and through which a sample and a buffer solution flow; a sample collecting part provided at an end portion of the first flow passage and configured to collect the sample; electrodes disposed at both sides of the first flow passage in a second direction perpendicular to the first direction and configured to apply a voltage to the first flow passage in the second direction; second flow passages communicating with both sides of the first flow passage in the second direction, configured to accommodate the electrodes, and through which a second buffer solution flows; and partition walls fixed to communicating portions between the first and second flow passages with a predetermined bonding strength and configured to block movement of substances between the first and second flow passages. The partition walls are formed of a gel material having ion permeability.