Marine microbes control the flux of matter and energy essential for life in the oceans. Until now, the distribution and diversity of planktonic microorganisms above Fe-Mn crusts have received relatively little attention. Future deep-sea mining is predicted to affect microbial diversity. Here, we studied the ecology of picoplankton among pelagic zones of a Fe-Mn deposit region, at Rio Grande Rise, Southwestern Atlantic Ocean. We investigated microbial community composition using high-throughput sequencing of 16S rRNA genes and their abundance estimated by flow cytometry.The picoplankton populations were more abundant in epi- and mesopelagic waters, corresponding to the Tropical and South Atlantic Central Water masses. Bacterial groups related to heterotrophy, such as Oceanospirillales (Gammapoteobacteria), SAR11 (Alphapoteobacteria), Flavobacteriales (Bacteroida), and Rhodobacterales (Alphapoteobacteria), were the main representatives of the pelagic microbial community. Additionally, we detected abundant assemblages belonging to acetate-oxidizing manganese reducers, i.e., Alteromonas. No differences were observed in microbial community diversity among pelagic zones and water masses. These results provide the first insights into the picoplankton abundance, taxonomy and diversity, and ecological processes in the Rio Grande Rise of the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.