Phytoplankton data of 12 investigations from August 2009 to November 2010 of 4 stations at Nha Phu-Binh Cang transect, Khanh Hoa waters were analyzed in order to illustrate temporal and spatial variations in species composition as well as in structure of phytoplankton community. Average values of species numbers of shallow stations 4 and 5 (63 +/- 12 and 58 +/- 16 species with the depths of 2.5 m and 1.8 m, respectively) of Nha Phu estuary area which was strongly affected by river discharge were lower than those of deeper stations 2B and 3 (88 +/- 13 and 86 +/- 13 species with the depths of 19 m and 12m, respectively) in Binh Cang bay area. MDS-2D analysis showed the temporal variability in species composition and community structure as well at" both 4 stations because of the river discharge, tide and fluctuations of temperature and salinity, especially at station 5 in few months of rainy season. Small cell size-diatoms Chaetoceros spp., Skeletonema sp. were frequently dominance in density and biomass at the whole transect. Sometimes, however, the larger cell size-dinoflagellates such as Protoperidinium spp., Protoperidinium oceanicum, Gonyaulax sp., Ceratium furca increased their densities and became the highest portions of total biomass.