Microbial communities inhabiting sponges are known to take part in many important metabolic pathways, including nutrient cycles, and possibly also in the bioaccumulation of trace elements (TEs). Here, we used high-throughput, Illumina sequencing of 16S rRNA genes to characterize the prokaryotic communities present in the external cortex and internal choanosome of the bacteriosponge Chondrosia reniformis and in the surrounding seawater. Furthermore, we estimated the total mercury content (THg) in each body region of the sponge and in the corresponding microbial cell pellets extracted from each region. Fifteen prokaryotic phyla were detected in association with C. reniformis, 13 belonging to the domain Bacteria and two belonging to the domain Archaea. No significant differences between the prokaryotic community composition of the two body regions were found. Three lineages of ammonium-oxidizing organisms (Cenarchaeum symbiosum, Nitrosopumilus maritimus, and Nitrosococcus sp.) co-dominated the prokaryotic community of both body regions, suggesting ammonium oxidation/nitrification as a key metabolic pathway within the microbiome of C. reniformis. In the sponge fractions, higher THg levels were found in the internal choanosome compared to the external cortex. In contrast, comparable THg levels were found in the microbial pellets obtained from both body regions however, THg levels in these microbial fractions were significantly lower than those observed in the corresponding sponge fractions. Our work provides new insights into the prokaryotic communities and trace element distribution in different body parts of a model organism relevant for marine conservation and biotechnology, paving the way for scientists to deepen the possible application of sponges not only as bioindicators, but also as bioremediation tools of metal polluted environments.