The present study provides the first information about diversity and abundance of microbial communities in two environments of the Argentinian Sea by the 454 - tag pyrosequencing technique. We observed more than 4,600 unique bacterial sequences from 36,188 tag amplicons, forming 280 phylotypes. In addition, nearly 2,700 unique sequences from more than 47,700 tags identified as Archaea, defined only 5 different phylotypes. The Jaccard distance (0.6 for Bacteria and 0.2 for Archaea) indicated higher differences among Bacteria rather than among Archaea in both studied sites. The dominant phylotypes in marine environment were Bacteroidetes Flavobacteriaceae, Proteobacteria Gammaproteobacteria, Proteobacteria Rhodobacteraceae and Proteobacteria Rickettsiales SAR11; and Pseudoalteromonadaceae Pseudoalteromonas, Proteobacteria Gammaproteobacteria, Proteobacteria Shewanella, Proteobacteria Rickettsiales SAR11 in the estuary sampling site. Archaea Euryarchaeota and Archaea Crenarchaeota were the major archaeal phylotypes found. The most abundant tag sequences included previously characterized taxa, although we also retrieved a large number of highly diverse, low-abundant phylotypes which constitute a largely unexplored "rare" biosphere. These microorganisms could have a crucial ecological role