In this study, we investigated the effect of tank disinfection technique on the bacterial profile of Gilthead seabream (Sparus aurata) larvae (L) and rearing-water (W) from a commercial fish farm using next generation sequencing of 16S rRNA amplicons. Three different techniques of disinfections were used in the rearing tanks: 1) Chlorination (24hrs) with a set of disinfectants and nebulization with active agent: acetic acid/hydrogen peroxide, Phosphoric acid Sodium hypochlorite/Sodium hydroxide and Didecyl Dimethyl Ammonium Chloride/Polyhexamethylene biguanide hydrochloride (Dis1). 2) Chlorination (24hrs) with Vircon wash, with active agent Potassium peroxymonosulfate/Sodium chloride and 1-week dry period (Dis2). 3) Chlorination (24hrs) with Vircon wash with active agent Potassium peroxymonosulfate/Sodium chloride and 50days dry period (Dis3). For further comparison, the bacterial communities at eggs stage and feed at different larval stages were also included in the investigation.