In order to investigate the differences in water quality and phytoplankton diversity between two depth ponds and provide the theory basis about transforming traditional pond into deep pond,an experiment was carried out to analyze the composition,distribution and community structure of the phytoplankton and physical and chemical indexes in three shallow pond (1.3±0.1) m and in three deep pond (2.2±0.1) m in Zhuhai Zhishan aquaculture base. The results indicated that the density,composition and predominant species of phytoplankton were significantly different between two depth ponds. The density,richness index,diversity index and evenness index of phytoplankton in deep pond were significantly lower than those in shallow pond. The contents of total phosphorus (TP) and total nitrogen (TN) were also significantly different between ponds. The contents of TP and TN in deep pond were significantly higher than those in shallow pond. The significant correlations between the density of phyloplankton and the contents of TP or TN were found in deep pond,but not in shallow pond.