The mat forming bacteria covering organic matter-enriched and anoxic marine sediments underlying a salmon farm in Southern Chile, were examined using 16S rRNA gene phylogenies. This mat was absent in the sea bed outside the direct influence of the farm (360 m outside fish cages). Based on nearly complete 16S rRNA gene sequences (-1500 bp), mat-forming filamentous cells were settled as the sulphur-oxidizing and putatively dissimilative nitrate-reducing Beggiatoa spp., being closely related (up to 97% sequence identity) to Beggiatoa spp. identified in eutrophic shallow sediments in northern Europe (Danish Limfjorden and German Dangast inlets). Their phylogenetic affiliation was consistent with their morphology as vacuolated and sulphur-containing cells arranged on tandem along trichomes (18 to 28 μm diameter). Additionally, deltaproteobacterial sulphate reducers, Sulfurospirillum, Sulfurovum and Fusibacter were detected according to partial 16S rRNA gene sequences (-500 bp). Their concurrence with Beggiatoa suggested an intense and complex sulphur cycle within the surface of these aquaculture-affected sediments, which may have important implications for the necessity of more efficient benthic-bioremediation of finfish aquaculture in Chile and worldwide.