Picocyanobacteria are abundant throughout the world’s oceans. Particularly, it has been reported thatSynechococcusstrains have a wide latitudinal distribution, from polar to tropical waters. However, their molecular characterization in the Southwest Atlantic Ocean is still missing. We analyzedSynechococcusgenetic diversity in a sector of the Argentine Sea, one of the richest biological areas of the world oceans.16S rRNAamplicons obtained after PCR amplification of environmental DNA extracted from water samples of this area were used for DGGE and sequenced. OnlySynechococcussequences could be retrieved. On the other hand, we isolated twoSynechococcusstrains from the environment. Our analyses revealed that the clade I group was widespread from latitude 38°S to 48°S and that can coexist with clade IV strains in shelf waters. The cooccurrence of these two clades may be related to an adaptation to high-nutrient/low-temperature waters. Our data are the first report onSynechococcusecotypes that would be important contributors to phytoplankton biomass in the Argentine Sea, one of the richest biological areas of the world oceans.