Larviculture represents a complex rearing ecosystem that involves various components, including larvae, rearing water, provided feed, and organic matter. The characteristic and the interactions between these components make it a favorable environment for the proliferation of undesired microorganisms that have the potential to adversely affect the health of the reared larvae. In the present study we investigated the bacterial communities associated with symptomatic Gilthead seabream (Sparus aurata) at the early larval stage (3-8dph, 11-14dph and 18dph) in comparison to their healthy counterpart. Furthermore, we explored the potential interplay among larvae microbiomes and the surrounding environment including rearing water, provided feed and organic matter, to shed light on connections occurring between the different microbiomes.