To know better the current situation of phytoplankton resources in middle-low reaches of the mainstream Yangtze River, we investigated the spatial distribution characteristics of phytoplankton in Wuhan-Estuary reach of the Yangtze River in the summer of 2014. Samples were collected from 19 sections. Investigation results show that there were 6 classes of phytoplankton detected, including 66 species been recorded, among which species of Bacillariophyta and Chlorophyta were recorded 24 and 23, respectively. Predominant species were recorded 3 classes, 6 species. The average phytoplankton cell abundance in Wuhan-estuary reach was (13.43±5.34)×10⁴ cell/L, with the maximum (23.18×10⁴ cell/L) recorded in upstream Wuhan and the minimum (5.19×10⁴ cell/L) recorded in the estuary at Shanghai. The average of Shannon’s diversity index was 3.37±0.35, the maximum was 4.1 recorded in downstream Nanjing and minimum 2.7 recorded in upstream Shanghai. Results of similarity clustering indicated that the phytoplankton communities at Wuhu-Nantong reach were similar, downstream Wuhan-Datong reach were similar and the phytoplankton community at upstream Wuhan was similar to that at upstream Shanghai. The study results suggest that the quantity and spatial distribution of phytoplankton in Wuhan-estuary reach of Yangtze River are probably affected by the hydrological conditions rather than the nutrition.