The FACS Canto II is an easy to use, powerful, and productive instrument that allows the counting of cells smaller than 5 µm in a water sample. It is equipped with 3 lasers (blue 488 nm, red 633 nm and violet 405 nm) that impact with each individual cell and separate them according to their fluorescent properties. This allows the identification and count of wide groups of pico-phytoplankton, heterotrophic prokaryotes (bacteria, archaea, flagellates) and even viruses in seawater samples, as well as the extraction of single microbial cells at multiple levels.