The yellowtail (Seriola lalandi) has been farmed for many years and is becoming a promising aquaculture species. Knowledge of the intestinal microbiota of this species is very limited. Thus, the aim of this study is to describe the bacterial populations associated with the intestinal tract of Seriola lalandi reared in Chile. The microbiota composition was analyzed at two growth stages distinguished by weight and parameters such as Specific Growth Rate (SGR) and Feed Conversion Ratio (FCR). Juveniles (mean initial weight 7.33 ± 0.30 g) and pre-adults (81.7 ± 19.0 g) were fed with commercial diet for 33 and 50 days, respectively. The first intestinal samples were collected at the end of Trial 1 from specimens weighing approximately 50 g while the second samples were obtained at the end of Trial 2 from specimens weighing approximately 370 g. The microbiota composition was examined using conventional isolation in Tryptic Soy Agar (TSA) followed by 16S rRNA sequencing and identification. In total, 16 genera were identified. Pseudomonas, Vibrio and Staphylococcus were the predominant genera in fish at the 50 g stage, whereas Microbacterium and Francisella were the predominant genera in the 370 g stage. The microbiota composition showed different assemblages, depending on host size, with Bacillus and Vibrio being the only genera that were shared. Knowledge of the intestinal microbiota of Seriola lalandi is the first step in the exploration of microbiota management and the development of probiotics, as well as in the identification of the bacterial populations in healthy fish under cultured conditions.