The reef ecosystems of Morro de São Paulo are located in the Tinharé-Boipeba Environmental Preservation Area which was established in 1992 in the state of Bahia, Brazil. Despite this area has been created more than two decades ago, no study has provided knowledge on the invertebrate biodiversity associated with such reef ecosystems. The present investigation provides the first inventory of benthic mollusks associated with the reef ecosystems of Morro de São Paulo based on the collection of living specimens and fresh empty as well as some worn shells. Mollusks were sampled in January 2015 and August 2016 through intensive searches from the intertidal to shallow subtidal habitats of the reefs on three beaches of Morro de São Paulo. Taxonomic richness and biodiversity indices were analyzed. This rapid assessment of the malacofauna resulted in the determination of 84 species belonging to 44 families of gastropods as well as 13 species belonging to eight families of bivalves and one chiton (total: 98 species). Species richness was numerically dominated by members of the subclass Caenogastropoda. The families with the largest number of species were Ranellidae (5), Muricidae (6) and Marginellidae (7). Conus regius, Cypraecassis testiculus, Lobatus goliath, Strombus pugilis, Tonna galea, Turbinella laevigata and Vasum cassiforme are extremely vulnerable macrospecies in the region due to their commercial importance. Comparisons of the malacofauna composition between the study site and Abrolhos Bank were made from data published for this region. ACE and CHAO 1 estimated 133 mollusk species for the region. Despite the rapid assessment, the number of species discovered in the study area approached 73.6% of the estimated total number. The considerable number of mollusk species found in a relatively small area with insufficient sampling underscores the importance of the reef ecosystems of Morro de São Paulo as a one priority area for conservation on the coast of the state of Bahia, Brazil, for which the species richness of other invertebrate groups is virtually unknown.