Phytoplankton plays an important role as primary producer and denotes the fertility of territorial waters. Samples were taken from a fishpond and estuary on August 27th, 2016 at Subang, West Java. The purpose of this research was to understand how the distribution and community structure of phytoplankton on fishpond and estuary differ. The result showed that phytoplankton found were composed by 6 classes: Cyanophyceae, Euglenophyceae, Chlorophyceae, Bacillariophyceae, Dinophyceae, and Xanthophyceae. Dinophyceae was found only in estuary, and Xanthophyceae was found only in the fishpond. Index of diversity (H') in the estuary was 2.41 and value of evenness (E) was 0.73. In fishpond, the value of H' was 1.63 and the value of E was 0.59, which shows no significance difference between the two locations. However, there was a difference between the number of Bacillariophyceae and Euglenophyceae found in both locations, and the difference between classes of phytoplankton found shows there might be some relations to the environmental parameters.