To investigate the role of microbial communities on the rate of mercury methylation, and in opposition, the impact of mercury on the diversity and activity of sedimentary bacteria, two different experiments were achieved. First, laboratory incubations were performed on estuarine sediments collected in the Adour estuary (Southwest France) under various conditions (oxic, anoxic, sterilized). Second, to confirm the batch experiments, in situ cores experiments were performed to investigate potential methylation of mercury in the Thau Lagoon (South France). The microbial diversity and mercury-linked activities were also analyzed using DNA fingerprinting technique (T-RLFP) and mer genes analysis. The two sets of results exhibit equivalent net methylation yields for surface sediments indicating similar methylation potentials for sediments from the Adour estuary (1% for 12 hours incubation) and the Thau Lagoon (0.9% for 1 day incubation). Methylation rates in sediment slurries decrease with the incubation time pointing out the needed of kinetic laboratory studies to complete in situ experiments. Furthermore, mercury methylation was strictly observed in anoxic slurries and correlates to anaerobic bacteria activity.