This study aimed to map the world's scientific production of bacterial and fungal microbiota in mollusks. The research was carried out in the Web of Science database, using "Fungi AND Mollusk" and "Bacteria AND Mollusk" descriptors and publication time between 2001 and 2021. Indexes were built by years, countries, research areas, and two maps of the co-occurrence of terms. There was a progressive increase in the production of microbiota in mollusks, with more research on bacteria during the investigated period. China and USA were the countries with the highest percentage of publications. Research with fungi and bacteria accounted for 28.41 and 17.66% in China, respectively. While the USA, the percentage was 21.05% for fungi and 16.02% for bacteria. Areas such as marine and freshwater biology (24.77%), fisheries (23.86%), biochemistry and molecular biology (18.60%), and pharmacy (17.83%) showed a higher percentage of indexed articles. There was also a high concentration of deposits of publications in the immunology area for both themes. The groups formed for bacteria and fungi indicated that studies had described the immune responses of mollusks, the genetic aspects associated with their defense mechanisms, pathogen virulence factors, and symbiotic and pathogenic microbiota, highlighting genera Vibrio, Aspergillus, and Escherichia coli pathogenic pathotypes. The bacterial and fungal microbiota in mollusks have been studied in several areas of knowledge and have given rise to research that can support the proper management of mollusks, application in the pharmaceutical industry, and implementation of measures in public health.