For automating the operation of an electrophoresis apparatus and improving the throughput, the present electrophoresis apparatus has two platens capable of controlling temperature of electrophoresis plates placed thereon, a loading medium charging unit for sending a loading medium under pressure, a loading medium charging nozzle mechanism having a pair of nozzles connected to the loading medium charging unit, a pipetter mechanism for dispensing samples to sample dispensing openings of the electrophoresis plates placed on the platens, a stacker mechanism for storing sample plates, a loading buffer solution supplying mechanism, a loading buffer solution dispensing mechanism connected to the loading buffer solution supplying mechanism, a power unit for allowing electrophoresis separation for each electrophoresis plate placed on the platens, and a detector for optically detecting components migrating through each electrophoresis flow channel of the electrophoresis plates.