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An innovative hyperspectral LIDAR instrument has been developed for applications in marine environment monitoring research activities, remotely detecting the fluorescence spectra produced in the spectral interval between 400 nm and 720 nm. The detection system is composed by a custom made photomultiplier charge integrating and measuring (CIM) unit, which makes automatic background signal subtraction, and a liquid crystal tunable filter (LCTF). The new instrument therefore has hyperspectral resolution and allows automatic background subtraction; it is compact and automated by custom software that permit to adapt the instrument properties depending on the environmental conditions. Laboratory tests to characterize the instrument performance have been carried out, concluding that this sensor can be employed in remote sites for Chl-a detection.