Organic carbon in mangrove sediments originates from both local sources (mangroves, microphytobenthos) and tidal inputs (e.g. phytoplankton, seagrass-derived material). The relative inputs of these sources may vary strongly, both within and between different mangrove sites. We combined elemental (TOC/TN) and bulk delta13C analysis on sediment cores from various mangrove sites with delta13C data of bacteria-specific phospholipid fatty acids (PLFA) in order to identify the dominant carbon substrates used by in situ bacterial communities. delta13C values of each of these markers showed a range of 10% or more across the different sites and sampling depths, but generally followed the delta13C trend observed in bulk organic carbon. Several sediment cores show a strong vertical gradient in PLFA delta13C, suggesting a selectivity for algal-derived carbon in the surface layers. Our data demonstrate that the origin of bacterial carbon substrates varies widely across different mangrove sites, and imply that data on mineralization of organic matter cannot be directly incorporated in ecosystem carbon budgets without an estimation of the contribution of various sources.