A marine sediment survey beneath four salmon farms in southern Chile was conducted. 16S rRNA pyrosequencing-based analysis was used to study the taxonomy and diversity of bacterial communities in sediments. Samples were taken under farm cages (study site) and reference (control) sites at different seasons and productive periods. Families associated with phyla Proteobacteria and Bacteroidetes were the most abundant, representing on average 50.7% of the total bacterial community. Flavobacteriaceae was the single family observed in all samples and also the most abundant. Bacterial diversity and richness indices (Chao1, Shannon and PD) at the study sites during productive periods showed a broader range of values than those measured in control or resting stage samples. Also, a very low number of shared families (2/54), compared with those taken at control (13/31) and resting stages (13/45), was observed. Bray-Curtis clustering of libraries resulted in two main clades, one mainly represented by samples of the study site and productive states, dominated by Sulfurovum with low values for bacterial diversity and richness indices and a community structure related to sulphidic sediments, while the other clades, mainly composed by control and resting samples, resulted dominated by Flavobacteriaceae and exhibited higher values of diversity and richness.