Pico-size cells with a red fluorescence signature similar to marine free-living prochlorophytes have been detected by flow cytometry throughout the fresh and brackish waters of the Changjiang Estuary in August 2005. These cells could be discriminated from Synechococcus by their lack of orange (phycoerythrin) fluorescence, from Prochlorococcus by their larger side light scatter, and from picoeukaryotes by their smaller side light scatter and much lower red (chlorophyll) fluorescence. The maximum abundances of these Prochlorococcus-like particles reached 3×104 cells ml-1 in the low salinity zone upriver and declined rapidly seaward. While Synechococcus was scarce and Prochlorococcus vanished in the brackish regions, the Prochlorococcus-like cells overnumbered the picoeukaryotes and became the predominant pico-size auto- fluorescing particles there, implying they might play an important role in this estuarine ecosystem and worthy of further investigation.