Marine sediments harbor an outstanding level of microbial diversity supporting diverse metabolic activities. Sediments in the Gulf of Mexico (GoM) are subjected to anthropic stressors including oil pollution with potential effects on microbial community structure and function that impact biogeochemical cycling. Metagenomic analyses offer a significant insight into the potential metabolic capacity of the microbial community, including hydrocarbon metabolism and the use of alternative carbon sources to thrive under limiting growth conditions. We identified genes for methane, naphthalene and toluene degradation affiliated with Rhizobiales, Burkholderiales and Rhodocyclales. In addition, results point to amino acids metabolism is mainly related to sulfur reducing bacteria affiliated with Acidobacteria, Chloroflexi and Firmicutes, and may play a crucial role as a central carbon source to favor growth in the Southern GoM impoverished carbon environment. Furthermore, regarding central carbon assimilation pathways, we identified the TCA pathway as one of the core metabolic pathways, as well as , aspartate, glutamate, glyoxylate and leucine degradation pathways, also as part of the metabolic core across samples. These observations provide fundamental and unprecedented knowledge for the Southern GoM sediments as a baseline for future studies to model microbial community responses to environmental perturbations, as well as to develop more accurate mitigation and conservation strategies.