Arranging a pair of temperature control units (29, 131, 132, 50) on both sides of gel 1 and arranging light-transmitting slit 134 on one of the elements, irradiation of an excitation beam over the gel 1 and signal detection are practiced through the slit 134. Introducing dry air onto the slit part, mildew occurrence is prevented on the detecting part. Detecting the power level applied to the gel and calculating the temperature of the temperature control units so that the gel temperature might be a predetermined temperature, on the basis of the detected power level, thereafter carrying out the feedback control of the power level, the gel temperature can be controlled appropriately and strictly during electrophoresis in an automatic fluorescent electrophoresis system, so that high-speed analysis can be done highly reproducibly at a higher voltage applied even by SSCP.