Rodrigo de Freitas lagoon is an eutrophic aquatic environment. The waters from the lagoon are released to the sea at Ipanema and Leblon beaches, through Jardim de Alah channel. In this work, the influence of these waters on the bacterial communities of these beaches was investigated. Eleven sampling stations were set between the lagoon and the beaches, and the samples were analyzed by molecular and microbiological parameters. PCR-DGGE of the DNA extracted from the samples was performed using rpoB primers. Preliminary results indicate that all used approaches could reveal the influence of the lagoon on the beaches bacterial communities.