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To test the hypothesis of longitudinal variations in phytoplankton compositions from a eutrophic lake to its river downstream and determine the length of the transition zone, we applied functional groups as well as taxonomical methods to this coupled aquatic system, which is composed of the Dianchi Lake upstream and the Tanglang River downstream, by sampling at 9 stations during Microcystis blooms in the Dianchi Lake in 2013. The longitudinal variations in phytoplankton compositions from lacustrine species to fluvial species were reflected by: (1) the shift from Microcystis to Chlorococcales green algae and centric diatoms; (2) the shift from the dominance of codon M to the coexistence of a variety of coda without one outstanding codon; and (3) except for codon M, the shift from lacustrine coda (H1, L O , T) towards coda that are adapted to both lacustrine and fluvial circumstances (MP, X1, X2). The prominent difference of phytoplankton compositions between the Dianchi Lake and the lower reaches of the Tanglang River revealed that there was a transition zone in between. The upper and middle reaches of the Tanglang River with a length of approximately 26.4 km were considered the transition zone because: (1) the dominant lentic codon M in the Dianchi Lake disappeared at the lower reaches of the river; (2) the amount of codon P that is sensitive to stratification rose at the beginning of the river; and (3) the codon T, which is well adapted to the persistently mixed layer or epilimnia of lakes, lost a large number of biomass at the upper and middle reaches of the Tanglang River. In this study, we found that the eutrophic lake had a significant influence on the river downstream. In addition, we found that functional groups were sensitive to the changes of external aquatic conditions and helpful in determining the length of the transition zone. [ABSTRACT FROM AUTHOR]