This work combines a hyperspectral sensor and an unmanned aerial vehicle to detect and differentiate phytoplankton species from optical data in Patagonian fjords at local scale. The results show differences between in situ spectral signals, especially in the blue, green and red near-infrared spectra, distinguishing between diatom and dinoflagellate. These tools are useful especially in coastal areas where cloud cover and geographical heterogeneity make satellite data acquisition difficult.