Flow cytometer (FCM) can be used to obtain the muti-parameters of the light scattering and fluorescence of individual cell rapidly and conveniently. It has been more and more applied in oceanographic and limnological studies. The work principles of FCM and its applications in the ecological studies of nano- and pico-phytoplankton were introduced and reviewed based on some recent publications abroad and at home in this paper. By means of FCM, sub-populations of phytoplankton can easily be classified, counted and sorted, and then further studies of the adaptive ability and ecological responses of the sub-populations can be implemented. It was concluded that FCM would have a prosperous prospect in the studies of the primary production and the microbial food web in marine ecosystem.
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