Fluorescence detection module for detecting the fluorescence in the micro-chamber is a light source, and a collimating lens for condensing the emitted excitation light from the light source, the light and the dichroic mirror to the dyke for selectively transmitting or reflecting according to the wavelength, a dichroic by condensing the excitation light selected by the dichroic mirror to be irradiated to the sample in the micro chamber, and an objective lens for condensing the fluorescence generated in the micro-chamber by the excitation light irradiation, the focusing for focusing a selected fluorescence by the dichroic mirror to the dyke lens, and a fluorescence detection device that detects the fluorescence focused by the focusing lens. Then, the fluorescence detection system, a frame and at least one fluorescence detection module with the holder and is provided on the frame a plurality of micro-chamber of the holder for supporting the fluorescent detection module for microfluidic chip in which a plurality of micro-chambers are arranged that and a driving unit for reciprocating movement along the arrayed direction, is installed on the support frame so as to be movable, and the holder includes a guide for guiding the movement thereof.