Picophytoplankton are distributed worldwide and are ubiquitous in all types of waters of varying trophic state. They are the major players in carbon production and form the base of complex microbial food webs. It is generally known that picophytoplankton have a competitive advantage when nutrients are limited. In recent years, picophytoplankton (0.2-2μm) have received increasing attention in coastal and nutrient-rich waters. However, information on the dynamic of the picophytoplankton community and the response of picophytoplankton along the environmental gradient induced by river discharge are relatively scarce in the Pearl River Estuary (PRE). In this study, the abundance and distribution of picophytoplankton were studied in the PRE during two cruises in August 2010 (high river discharge) and January 2011 (low river discharge) using epifluorescence microscope technique. The associations between picophytoplankton, size-fractioned chlorophyll a and phytoplankton, salinity, nutrients and other environmental variables were examined. Multiple linear regression analysis was also used to determine which environmental factors were significantly correlated with the abundance of phytoplankton and picophytoplankton in the two distinct seasons. Our results showed that phytoplankton community generally was dominated by some freshwater algal species in the upper estuary while estuarine species Skeletonema costatum in the middle and downstream of the estuary. In the summer, phytoplankton density was significantly related with phosphate concentration and N/P ratios were much lager than 30 simultaneously. It suggested that the growth of phytoplankton was limited by P in the summer in PRE. Temporally, the averaged density of picophytoplankton was always higher in the summer (2.67×10⁴cells/mL) than in the winter (1.60×10³cells/mL), which probably due to high turbidity and low temperature in winter. Consistent with other studies, picophytoplankton abundance was positively correlated with temperature in PRE. It maybe reflect the growth of picoplankton was strongly dependent on water temperature. Picophytoplankton numbers in our study were much lower than that in the Chesapeake Bay, the Changjiang Estuary while higher than the Jiaozhou Bay. These differences may be attributed to various light regime, nutrient structure and zooplankton predation between these estuarine ecosystems. In the present investigations, picophytoplankton density was very low near the Humen outlet and increased along the salinity gradient, to reach its maximal value at southernmost stations in two seasons. The abundance of picophytoplankton was positively related with salinity and inversely with inorganic nutrients, implying the negative influence of the riverine and coastal waters on picophytoplankton and the oligotrophic ecological niche of picophytoplankton. And hence, it presented such spatial distribution pattern. As with picophytoplankton abundance, the proportion of pico-chl. a of total chl. a increased from the upstream of the estuary to the near-shore open water (Wanshan islands), where picophytoplankton growth was probably promoted by high light intensity and low levels of nutrients. The average and maximum proportion of pico-chl. a in summer was 11.9% and 26.3%, respectively. Our results suggested that picophytoplankton assemblage was an important primary producer in the PRE. Multiple linear regression equations of picophytoplankton revealed that phosphate and suspended solid concentration (SSC) were the crucial factors shaping picoalgae distribution in the PRE. In our observation, picophytoplankton was negatively related to phytoplankton, suggesteda potential competition between these two groups or their diverse ecological niches adapted to specific environment conditions. How light and nutrients involved in interaction of these two groups are considered as a direction requiring further research.