Macrobenthic communities were investigated in Pearl River Estuary in summer and winter 2006. A total of 245 species of macrofauna were identified in the two cruises (153 species in summer, 157 species in winter)，belonging to fish，Echinodermata，Crustacea，Nemertea, Mollusca，Annelida (Polychaeta and Oligochaeta), Coelentera, Plathyhelminthes, Sipuncula and Echiura. Polychaeta had the highest species number which included 140 species in the two cruises, with 91 species in summer and 93 species in winter, respectively. Apionsoma trichocephala, Parheteromastus sp., Notomastus latericeus, Cossurella dimorpha, Magelona sp., Sternaspis scutata, Aglaophamus jeffreysii, Paraprionspio pinnata, Prionospio queenslandica and Amphioplus laevis are the main dominant species in the investigated area of Pearl River Estuary. Apionsoma trichocephala was the most abundant species, distributing over the south and central area of Pearl River Estuary. The average biomass and abundance of total macrofauna were 14.313g/m2 and 205.3ind/m2 in summer, and 13077g/m2 and 168.8 ind/m2 in winter, respectively. Species number, biomass and abundance increased from inside Pearl River estuary to the open sea. CLUSTER analysis and multi-dimentional scaling （MDS） analysis indicated that macrobenthic communities were divided into three communities in summer, and five in winter. The biodiversity was the lowest in north of Pearl River Estuary in summer and winter. ABC (Abundance/biomass comparison curve) method was used to determine the levels of disturbance that macrobenthic communities were under. Macrobenthic communities were undisturbed in summer. The north stations of macrobenthic community I were under moderately disturbance in winter while other communities in winter were undisturbed. Pearl River freshwater input was the most important factor to influnce the distribution of macrobenthic communities. Correlation analysis showed that salinity and macrobenthic species number and biodiversity index (H′, J′ and D) were significantly positively correlated in summer and winter.