Flow cytometry (FCM) is routinely used in medical and veterinary diagnostics although it is also widely applied in environmental studies, including phytoplankton investigations. Cyanobacteria are wide-spread photosynthetic microorganisms that attract attention due to their ecology and potential toxicity. Therefore, novel research tools are being applied in their investigation. This paper characterizes FCM as a technique that enables photopigments (chlorophylls and phycocyanin) expressed by

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... bacteria to be excited and their emission to be subsequently detected. This feature not only allows cells to be counted in a rapid manner but also enables a wide range of potential applications in ecological and biochemical studies. The main advantages of FCM, such as rapid, automatic and precise measurements requiring small sample volumes, are also discussed in this paper along with challenges including analyses of filamentous cyanobacteria and signal overlapping. It is expected that FCM will continue to be used in some fields of cyanobacterial studies.