**Abstract**

Aquaculture is a rapidly expanding food production sector, facing the challenge of growth both increasing its efficiency and reducing its negative impact on the environment. Metagenomics is an emerging tool in aquaculture that helps to understand the complex host (fish-shellfish)-microbiota-pathogen-environment relationship underlying disease outbreaks, monitoring the dynamics of microbial diversity in farmed animals subject to different environmental conditions or perturbations. As Chile takes an important share of world aquaculture market, this chapter reviews the actual and potential applications of metagenomics to support a sustainable expansion and diversification of Chilean aquaculture. The focus is on (i) the role and function of the gut microbiota in the proper immunostimulation and disease control and (ii) the role of metagenomics in monitoring environmental microbial biodiversity and dynamics in relation to disease persistence and ecosystem stability. We conclude that despite the importance of the aquaculture sector in Chile, the application of metagenomics to deal with disease control and ecosystem preservation is still an emerging field of study. Understanding host (fish-shellfish) microbiota-pathogen-environment diversity of interactions in a more holistic view, i.e., the holobiome approach, could be key to develop rational strategies to improve productivity by increasing resistance to diseases and reducing the use of antibiotics and their negative environmental impact.

**Keywords:** metagenomics, Chilean aquaculture, microbiota, disease, environment
