Assessments of picoplankton carbon biomass in the pelagic ecosystem over the deep region of the southern Gulf of Mexico were conducted during three consecutive summer cruises. Notably, the relationship between carbon distribution of Prochlorococcus (PRO) and Loop Current (LC) dynamics was evaluated. Seawater samples were collected from the euphotic zone (~150 m) for estimating the abundance of the picoplankton populations using flow cytometry analyses. Carbon biomass estimates were based on cell abundance and variable conversion factors computed across stations and depths. On average, about half of the total depth-integrated carbon biomass of picoplankton was attributed to heterotrophic bacteria (HB, 54%) and three autotrophic populations (Prochlorococcus, Synechococcus, and pico-eukaryotes, 46%). In agreement with previous winter assessments, PRO was the dominant component of abundance (~90%) and picophytoplankton community biomass (>70%). Based on molecular analyses, distinct ecotypes of high-light PRO and low-light (LL) PRO were found within the euphotic zone, vertically distributed along light and nutrient gradients. Also, PRO distributions were related to hydrographic conditions strongly modulated by mesoscale dynamics. LL-PRO subgroups, located close to the nutricline under LL conditions, were associated with the westward propagation of anticyclonic eddies that episodically detach from the LC. This study highlights the role of the LC and its eddies in the transport and distribution of carbon biomass into the Gulf of Mexico, as represented by the deep subgroups of the dominant, tiniest autotroph within this oligotrophic ecosystem.