Trace elements are ubiquitous substances in the marine environment, representing a problematic hazard for organisms since many of them lack any biological function. The main aim of the study was to investigate the variation of the total mercury content (THg) in the Mediterranean sponge Chondrosia reniformis collected in two islands of the Tuscan Archipelago, Italy. The two islands did not show harmful levels of THg (seawater and sediment) and no intraspecific variability was detected in THg values and bioconcentration factors of collected samples. Conversely, THg values recorded in the choanosome of C. reniformis were significantly higher than in the cortex, pointing out a possible involvement of the sponge microbiota in the bioaccumulation process. Our study suggests that C. reniformis could be an attractive bioindicator of toxic elements pollution in coastal waters, highlighting the potential use of these organisms in the monitoring programs of coastal areas, as suggested by various European marine policies.