Xianshan Bay (121°25′–122° 03′E, 29°05′–29°46′N) is located in the middle of Zhejiang province along the coast, a long and narrow semi-closed bay with the water area of 1 445 km², and average water depth of 20 m. In recent years, the scale of aquaculture became larger and larger, and with pollution from land-based source, which made the environment in this bay increasingly 2009–2011, we expanded the scale of macro-algae culture near the cage area of middle Xiangshan Bay to try to restore the habitat around the areas of cage culture. To assess the response, we measured the characteristics of the bacterial communities in the sediment of using PCR, denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. The bacterial communities in the sediment environment of the cage culture area consisted primarily of 7 phyla lineages of the domain bacteria. There was an increase in bacterial diversity during restoration and the dominantAcinetobacter. sp. DSW4-37, bacterial community in the algal culture area consisted primarily of 5 phyla lineages of the domain bacteria and the . RDA analysis revealed that influencingThe improving trend in bacterial communities was consistent with improvements in chemical indices. the use of macroalgae to restore the , and bacterial community structure can be used as an index to evaluate the effectiveness of habitat restoration.