The Gulf of Mexico (GoM) is exposed to a continuous hydrocarbon presence, which influences the microbial community composition. In order to get an overall view of this geographical zone, we have carried out a metagenomic assessment of the bacterial community and searched for metabolic markers that could contribute to explain how the GoM microbial community participates in biogeochemical cycling. Two separate sites, one in the north-west (NW) and one in the south-east (SE) of the GoM were analyzed showing differences in their microbial composition and metabolic potential. This shows the delicate equilibrium that sustains microbial communities and how currents, climate, rivers, faults, and other natural processes, and pollution or anthropogenic actions can impact microbial profiles and therefore their role in the biogeochemical cycles.