The culture of aquatic organisms is still hampered by the occurrence of unpredictable diseases in their early life stages, which are responsible for massive mortalities and considerable economic losses. A better understanding of the host–microbe interactions is certainly essential to develop effective solutions of disease control for the aquaculture industry. As demonstrated in terrestrial animals, the use of gnotobiotic systems (animals cultured in axenic conditions or with a known microflora) can be an excellent tool to extent the understanding of the mechanisms involved in host–microbe interactions and to evaluate new treatments of disease control. Several aquatic animals were cultured so far in germ-free conditions, such as fish, molluscs, crustaceans, rotifers, echinoderms, cnidarians, turbellarians, ascidians and echiurans. The aim of the present review is to recapitulate the findings obtained with gnotobiotic aquatic animals over the last decades, with special emphasis to the host–microbe interactions, as well as the perspectives for future research in this field. In addition, the procedures utilized to culture axenic aquatic animals and to verify contaminations are summarized, and the standardization of these procedures is proposed.