Underwater hydrothermal vents draw a lot of interest as they are the shelter for unique ecosystems, besides being a possible new opportunity for ore mining. Manganese (Mn) is found at a high concentration in hydrothermal vents, which make it possible to use this metal ion as a tracer to detect and evaluate new hydrothermal sources. Here we present a miniaturized and integrated microfluidic system for the detection of Mn in deep-sea environment, called the integrated in situ analyzer for Mn2+ (IISA-Mn). The detection system is based on the chemiluminescence reaction of Mn contained in the seawater sample with a luminol-based reagent, which offers a high sensitivity. This system is composed of a microdevice for mixing and reaction, a pumping unit, several valving units, and a photomultiplier (PMT) detector. The system is able to detect Mn concentration above 280 nM in seawater, and gives a quite linear response until 500 nM. It is also proven to be able to work continuously during the 8 h of an actual remotely operated vehicle (ROV) dive. This system has led to the discovery of a previously unknown hydrothermal site in the Okinawa Trough.