This study aimed to describe the surface microbiomes from 4 remote points in the Argentine sea and 3 freshwater bodies in the Argentine Pagatonia using 454 high-throughtput sequencing. The Argentine shelf in the Southwest Atlantic Ocean is one of the largest and most productive continental shelves of the World. Notwithstanding that, microbiological studies of this region are scarce. Likewise, the microbiomes of most Patagonian freshwater bodies have not been studied using culture-independent methods.