Abstract:The variation of amount and community composition of bacteria in the sea water and sediments of monoculture (Apostichopus japonicus) and co-culture systems (A. japonicus co-cultured with Gracilaria lemaneiformis) were evaluated. The total numbers of bacteria (2.14×106~4.27 ×106cells/ml) in the bottom water of the monoculture and co-culture systems increased during the period of the experiment. The bacteria numbers in the surface sediments ranged from 1.55 ×108 to 3.39 ×108cells/gdw in the systems, which were much higher than those in the bottom sea water. UPMGA cluster analysis of DGGE fingerprint from sediments revealed the bacterial community in the same sampling date had higher similarity than those in different sampling dates. Phylogenetic analysis showed that the dominant bacteria of the sediment in the monoculture and co-culture systems belong to α-proteobacteria, γ-proteobacteria, δ-proteobacteria and bacteroidetes.