ABSTRACT: A pelagic bacterial community structure was examined in experimental intensive shrimp culture ponds that have a shrimp–mangrove complex aquaculture system, an extensive shrimp culture pond and a mangrove area in Thailand by denaturant gradient gel electrophoresis analysis of polymerase chain reaction amplified partial 16S rRNA genes. Bacterial community structure in the intensive shrimp culture ponds was distinguishable from that of the mangrove area. In the extensive shrimp culture pond, the bacterial community structure resembled that in the mangrove area, but bacterial abundance was as great as that in the intensive shrimp culture ponds. Among the intensive shrimp culture ponds, the bacterial community structure was different between a closed culture system and a shrimp–mangrove complex culture system. Moreover, the bacterial community structure in mangrove planted ponds was close to those in the intensive shrimp culture ponds when shrimp culture was conducted, but it was close to those in the mangrove areas without shrimp culture. These results suggest that intensive shrimp culture with shrimp feed input affects the bacterial community structures in pond water.