Among the ecosystem services provided by the seagrass Posidonia oceanica, its role as a carbon sink has received growing attention during the last decade. The sequestration and stabilization of carbon in soils are tightly linked to the activity of its microbial community. EcoPlates (Biolog) comprise a semi-quantitative tool for the assessment of microbial functional activity that generates profiles of microbial carbon source utilization. In this study, the aerobic and anaerobic carbon consumption in a healthy P. oceanica meadow was compared throughout depths down to 130 cm. After 11 d, the average well color development, Shannon-Wiener diversity index (H’), and kinetics of carbon consumption were assessed. Both the aerobic and anaerobic metabolisms showed carbon consumption at all depths. Color observations indicated that carbohydrates, amino acids and polymers were mainly consumed, while carboxylic acids, amines and miscellaneous compounds presented low or no consumption at all. Carbon consumption kinetics were similar for both metabolisms. The results suggest a pronounced stratification of the microbial community controlled by oxygen availability. Despite the higher aerobic metabolism in the top 40 cm, the anaerobic metabolism was dominant, supporting high sequestration of carbon in P. oceanica meadows.