The effects of polyculture tanks on the gills and intestines microbiome of two fish species endemic to the Sao Francisco river, namely, Rhinelepis aspera and Prochilodus argenteus, were tested. This is the first predictive study of microbial diversity by 16S gene metagenomics in fish species from the Sao Francisco river and from a hatchery. The study goal is to improve aquaculture production for fish farming and repopulation of wild animals.