© 2017 Wiley Publishing Asia Pty Ltd. Micro-organisms are an essential component of natural marine ecosystems, but also play important roles in anthropogenically modified ecosystems, including aquaculture. Although metagenomics is currently used to explore microbial communities, its application has not been as extensive in aquaculture. Although some taxonomic profiles and phylogenetic studies have been deciphered using biomarker genes, the functional potential of microbial communities associated with aquaculture systems is still unknown in most cases. Predicting functional profiles through 16S rRNA gene-based metagenomics analysis is perhaps the most promising tool to elucidate the metabolic capabilities of microbial communities because there is no need to perform shotgun sequencing to have an idea of these capabilities. Moreover, robust bioinformatics background is not required to assess this information, and so the same data (16S rRNA sequences) are used to estimate both taxonomic and functional profiles, therefore providing deeper insights into these kinds of communities. In this review, we suggest the need to major use of novel bioinformatics tools that construct functional profiles from metagenomic 16S rRNA data, as strategy to obtain a preliminary approach about metabolic capacities of microbes that coexist in aquaculture systems.