Marine sponges are known to carry out several processes that contribute to the functioning and health of the benthic ecosystems. They also harbor diverse microbial communities in which complex interactions are established and aid the host to grow and develop. Despite the contribution of prokaryotes for host health and stamina, we lack evidence of how these com-munities are structured when associated with marine sponges from the coast of Sao Paulo, a region that can be considered as a hot spot of sponge diversity in Brazil. To tackle this, the sympatric species Aplysina caissara (endemic), Axinella corrugata and Dragmacidon reticu-latum were collected along with surrounding seawater and sediment at Guaeca region, in the north coast of Sao Paulo. The sponge species were identified using morphological characteris-tics and by barcoding using the cytochrome b (cob) gene. The DNA from the sponges, sea-water and sediment were extracted and subjected to Illumina MiSeq platform using the 16S rRNA gene. The cob gene was able to separate A. caissara from other Aplysina species. Overall, 64 prokaryotic phyla were detected and among them the most abundant were Proteo-bacteria Bacteria unclassified Cyanobacteria Crenarchaeota Chloroflexi, and Acidobacte-ria. Surprising was the high percentage of OTUs that could only be assigned to the Bacterial domain, suggesting the recovery of novel unidentified taxa. The prokaryotic communities were species-specific and distinct from the environmental samples. Between 56 and 80% of the OTUs was specific to each host sponge. Fifty-four prokaryotic members were responsible for the differences detected among the categories. Besides, functional prediction performed with Tax4fun2 demonstrated that A. caissara was enriched for energy metabolism (carbon, nitrogen, sulphur and methane cycling) and biosynthesis of secondary metabolites, whereas D. reticulatum was enhanced for metabolism of terpenoids and polyketides, and xenobiotics biodegradation and metabolism. This survey showed that each sponge species harbours its own prokaryotic communities and that members responsible from the differences among sponge species could be related to the predicted functions.