The microbiota is a complex of microorganisms associated with a specific habitat, which influence the performance, welfare, and numerous host functions, such as development, digestion, nutri-tion, disease resistance, and immunity. Cobia is a tropical fish species, which has been studied for its potential for marine aquaculture, however, the study of microbiota (bacterial community) has been underreported and there are no reports of the mycobiota (fungi community). In this study, we characterized the intestinal microorganism profile of cobias fed two types of diet by next generation sequencing (NGS) of the 16S rRNA and ITS region. The microbiota showed a higher abundance of the phylum Proteobacteria (~96 %) and Firmicutes (~1 %). In addition, a higher abundance of 11 bacterial genera, mainly Oscillospiraceae UCG-002 and Faecalibacterium, was ob-served in cobia fed with formulated feed (FF). While a higher abundance in 8 genera, mainly Haemophilus and Actinobacillus, was observed in cobia fed with frozen fish pieces (FFP). The functional characteristics of cobia were associated to metabolism, environmental information processing, and cellular processes in (Orthologous KEGG groups) KOs level 1, without differ-ences between diets. The mycobiota showed a higher abundance of the phylum Ascomycota (~88 %) and Basidiomycota (~11 %). No differences were found in the mycobiota. Finally, further studies on mycobiota are recommended, since very few have been reported in fish, despite the role that fungi play at the intestinal level.