Phytoplankton is composed of major primary producers, but also harmful algae that can negatively influence marine environment. Many programs have been developed to monitor toxic phytoplanktonic microalgae in coastal waters. Water samples were collected from the water column for phytoplankton observation, fixed immediately with neutralized formalin, and concentrated by sedimentation. The main advantage of the immunological techniques is the wide variety of immunoglobulins for the specific detection of different targets characterizing by sensitivity, specificity, and fast performing. Population genetic studies, taxonomic identification, and environmental monitoring are hampered by two major constraints: the necessity to establish monoclonal cultures from environmental samples and the sensitivity of available molecular tools. Phytoplanktonic samples have to be representative of the water column and provide information on the presence of toxic species as well as on population trends. Most detection tools used for phytoplankton rely on detecting nucleic acids because of the instability of other molecules such as ribonucleic acid and proteins.