The presence of cyanobacteria in the intertidal zone is strongly influenced by changes in physical and chemical parameters. In milkfish ponds, cyanobacteria community had been indirectly affected by the mixing of sea water and fresh water during low tides. To determine the relationship between the cyanobacteria community and water quality parameters, phytoplankton samples were taken both vertically and horizontally in three fish ponds at Blanakan Village on July and August 2016. The water quality parameters measured were temperature, DO, salinity, and pH. Based on the enumeration results of 36 samples of phytoplankton, 5 genus Cyanobacteria (Merismopedia, Microcystis, Lyngbya, Oscillatoria and Trichodesmium) were obtained. Cyanobacteria is a subdominant group after diatomae with dominance index between 2-21 %. Average of density ranged between 128-3563 plankters /10 dm3. High dominance level (97-99 %) between cyanobacteria and diatoms cause phytoplankton diversity indices in all three fish ponds were very small (0.0851 to 0.8734). Based on the analysis of the three main components (Principle Component Analysis) it was known that the presence of five cyanobacteria genus was determined by the differences of water quality parameters observed. Merismopedia was more affected by salinity and DO fluctuations. Oscillatoria, Trichodesmium and Lyngbya were determined by changes in temperature, whereas Microcystis was more affected by pH.