In Southeastern Brazil ecoregion, the assessment of calcareous sponges diversity has been particularly focused on Rio de Janeiro State, with 26 species recorded, while São Paulo State remains relatively unexplored, with only 11 species known up to date. São Sebastião, located on the northern coast of São Paulo, encompassing the Alcatrazes Archipelago, is an area of high ecological relevance. This study investigates the diversity of calcareous sponges within two Marine Protected Areas in São Sebastião region, integrating morphological and molecular approaches. A total of 18 species were identified, including two of the subclass Calcinea and 16 of the subclass Calcaronea. Among them, six are new to science: Ascandra arenaria sp. nov., Amphoriscus tenax sp. nov., Leucandra anoducta sp. nov., Leucosolenia sebastianensis sp. nov., Sycon caissarum sp. nov., and Sycon crassapicale sp. nov. Additionally, other eight species represent new records for São Paulo, with Leucandra caribea being reported for the first time in Brazil, extending their distribution ranges. The remaining four species had previously been recorded in the region. Furthermore, as an important additional morphological character, we are originally reporting the presence of a few tetractines, alongside triactines, in the atrial skeleton of the invasive species Paraleucilla magna. Our findings provide a comprehensive baseline inventory of calcareous sponge species from the São Sebastião area (Ilhabela and São Sebastião, including the Alcatrazes Archipelago) and contribute to understanding the biogeographical affinities of the calcarean fauna of Southeastern Brazil with regions within and beyond the Atlantic Ocean.