Abstract: To study the community structure and species diversity of diatom in downstream of Jialing River, 8 diatom samples were collected according to normal methods, in October, 2006, February, May, and December, 2007, respectively. Diatom species numbers, cell density, diversity index, evenness index and diatom quotient were studied as well as water quality was analysed according to diversity index and diatom quotient. The results showed that: (1) 89 taxa, which belonged to 2 class, 11 family and 22 genera, were observed (including variety and form). Pennatae diatom species richness were higher than that of centriate diatom; The cell densities of diatom was in the range of 0.57×104—4.51×104 ind/L with the mean value of 2.3×104ind/L; The diversity index was in the range of 0.72—3.12 with the mean value of 2.20; The evenness index was in the range of 0.15—0.52 with the mean value of 0.36; The diatom quotient was in the range of 0.66—9.48 with the mean value of 3.24. Compared with Daning River, Han River, Yangtze River, and so on, diatom community structure in downstream of Jialing River took on higher species richness and diversity and lower cell density. (2) The diatom community structure took on noticeable seasonal and horizontal distribution distinction. To seasonal change, Spring (Feb., 2008) and Autumn (May, 2008) had higher species richness, cell densities, diversity indices than those in Summer (Aug., 2008). To horizontal distribution change, from upstream to downstream, the diatom species richness and diversity indices declined gradually, however, cell densities and diatom quotient increased gradually. (3) The water quality in downstream of Jialing River belonged to β-mesosaprobic Zone totally. The water quality of the sampling sites in upstream city was better than those in downstream city. The water quality of YM, SX, WTX and JK was better, which belonged to β-mesosaprobic Zone or Oligosaprobid Zone; Those of HC, MBT, CQK and CTM belonged to α-mesosaprobic Zone or Polysaprobic Zone.