Fluctuation of phytoplankton community in rotational rice-tiger shrimp systems was investigated during a period of August 2013 to August 2014 mainly in Ca Mau, Kien Giang and Bac Lieu provinces. In the system, there were two rice fields with the area of 2,500-5,500 m2 each. Qualitative and quantitative samples were taken 6 times throughout the production period including the beginning, the middle and the end. A total of 9 samples were collected at each time for all three sites. Data revealed that a total of 145 species were recorded in which Euglenophyta was the most populated, 44 species (covering 30.46%), followed by Diatom (37 species, 25.37%). The rest groups were only accounted for 4-5%; The common species found in sampling sites including Nitzschia, Synedra, Cyclotella, Thallasiosira  (Diatom), they are important  food group of algae in water bodies (Ryther et al., 1981; Boyd, 1990). To assess the nutritional condition in the rotational rice-shrimp model,  diatom quotient showed that all three farming sites of Ca Mau, Bac Lieu and Kien Giang are eutrophic with the nutritious value of 1 rice and 2 rice: 0.28; 0.36 (Kien Giang); 0.54; 0.57 (Ca Mau) and 2.2; 3 (Bac Lieu), respectively. There were many algae species indicator eutrophic conditions including Oscillatoria, Euglena, Scenedesmus, Navicula, Chlorella, Nitzschia and Ankistrodesmus, they tolerant to organic pollution. The score of Palmer index was ranging from 11-28 also indicating organic pollution. Highest densities recorded in Kien Giang, Ca Mau and Bac Lieu at the beginning of production period were 5,462,333 ind.L-1; 5,609,083 ind.L-1and 9,398,889 ind.L-1, respectively. Particularly, high densities of euglenoid indicating rices were contaminated by organic matter. However, the density of phytoplankton in all three sites tended to decrease at the end of production cycle.