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Objectives: To establish a diatom database by analyzing the quatity, species distribution and differences of diatom in water samples of the whole navigable sections of the Beijing-Hangzhou Grand Canal, to provide a reference for the inference of the drowning site., Methods: Water samples were collected at 22 sites in the navigable sections of the Beijing-Hangzhou Grand Canal (Jining section to Yangzhou Section), and the diatoms at each site were qualitatively and quantitatively analyzed by using graphite digestion-scanning electron microscopy., Results: Sampling site T (Laohuaijiang River Line, Gaoyou City, Yangzhou City, Jiangsu Province) had the highest number of diatoms, while sampling site O (Siyang County, Suqian City, Jiangsu Province) had the lowest number of diatoms, with a large gap of 68 times. At sampling site Q (Jiangpu District, Huaian city, Jiangsu Province), there were 19 species of diatoms. The sampling site O had the least diatoms, with 7 species. There were no significant differences in species evenness and species diversity at each sampling site ( P >0.05). Some sampling sites have characterized diatoms, such as Caloneis at station A (Taibai Lake, Weishan County, Shandong Province), Rhoicosphenia at station B (Nanyang Town, Weishan County, Shandong Province), Amphora at station I (Taierzhuang District, Zaozhuang City, Shandong Province) and Epithemia at station J (Pizhou 310 national highway, Xuzhou City, Jiangsu Province)., Conclusions: The species richness of diatoms gradually increased from north to south. Diatom species richness and species diversity might be higher in areas with complex environments and large population flow. Climate type has a certain influence on the distribution of diatoms.