In August 15-28, 2009, a preliminary study was conducted on the spatial distribution characteristics of heterotrophic bacteria (HB), inorganic phosphate bacteria (IPB), organic phosphate bacteria (OPB), denitrifying bacteria (DB), and ammonifying bacteria (AB) in the hypoxic zone of Yangtze River Estuary. In the water surface, water bottom, and sediment surface of the zone, the average quantity of AB was the largest, being 307.52 x 10(4) cells x L(-1), 184.50 x 10(4) cells x L(-1), 199.97 x 10(2) cells x g(-1), followed by that of HB (87.35 x 10(4) cfu x L(-1), 86.85 x 10(4) cfu x L(-1), and 19.56 x 10(2) cfu x g(-1)), and of OPB (19.26 x 10(4) cfu x L(-1), 18.82 x 10(4) cfu x L(-1), and 19.56 x10(2) cfu x g(-1), respectively). IPB was only observed within the Yangtze Estuary, south passage of the Estuary, and Zhoushan inshore, and its average quantity in the water surface, water bottom, and sediment surface was 18.50 x 10(4) cfu x L(-1), 31.00 x 10(4) cfu x L(-1), and 7.17 x 10(2) cfu x g(-1) respectively. DB had a wide distribution, but its average quantity was low, being 3.94 x 10(4) cells x L(-1), 23.08 x 10(4) cells x L(-1), and 6.22 x 10(2) cells x g(-1) in the water surface, water bottom, and sediment surface, respectively. Salinity, NO3(-)-N, PO4(3-)-P, SiO3(2)-Si, and pH were the main factors affecting the distribution of HB, IPB, OPB, and DB in water body and sediment surface. The HB, IPB, and OPB in water bottom and sediment surface had significant positive correlation with water temperature; the HB and OPB in water bottom and the IPB in sediment surface were significantly positively correlated with dissolved oxygen (DO); while the AB in sediment surface was significantly negatively correlated with DO. Cluster analysis showed that hypoxia affected the bacterial community structure in sediment surface.