Flow cytometry (FCM) was used to examine the abundances and distributions of different picophytoplankton groups (i.e. Synechococcus, Prochlorococcus and picoeukaryotes), nanophytoplankton, heterotrophic bacteria and viruses were examined in the Changjiang Estuary, China and adjacent coastal waters during autumn 2004. Water temperature and light availability were found to be critical factors for picophytoplankton growth. Positive correlations were found between picophytoplankton, heterotrophic bacteria and viruses, and a seaward-increasing trend in the V-I (the group yielding high green fluorescence according to FCM) population within viruses was detected. The importance of nanophytoplankton is progressively usurped by picophytoplankton with increasing distance offshore. Picoeukaryotes are the most successful group among picophytoplankton in near-shore eutrophic waters, whereas Prochlorococcus surpasses other groups within the pico- and nanophytoplankton community in offshore oligotrophic regions of the East China Sea Shelf.