The bacteriological water quality associated with marine fish farming systems can be a determining factor in the development of disease, and understanding this quality is fundamental for the prevention and control of possible disease outbreaks. In the present study, the bacteriological water quality of a yellowtail amberjack Seriola lalandi broodstock maintenance system, composed of two units of a recirculation aquaculture system (RAS 1 and RAS 2), was determined. From February 2016 to January 2017, monthly samples of surface water were taken at six points in the two RAS systems: (a) from the water reception tank and (b) from filter 1 and (c) tank 1 (in RAS 1) and (d) filter 2 and (e) tank 2 (in RAS 2) and from a joint (f) discharge point. The bacteriological quality was determined by counting total heterotrophic bacteria (THB) and by molecular identification (16S rRNA gene). The number of THB showed a tendency to decrease in filters 1 and 2, to increase in tanks 1 and 2, and again increase in the discharge. The fluctuation of THB, in general, was from 1.0 × 103 to 2.9 × 105 CFU/mL. In total, 102 colonies were isolated, corresponding to nine orders and 52 species, and Vibrionales and Alteromonadales were the most abundant orders. The bacterium Vibrio harveyi, a pathogen of S. lalandi, was identified, as were other bacterial species that are known pathogens; however, no signs of disease or mortality events were recorded during the study. These results suggest that the bacterial community contributed to the maintenance of a balance in the RAS, which prevented the development of infectious diseases. Furthermore, the physicochemical parameters (temperature, oxygen, nitrogen compounds, and alkalinity) were maintained within the optimum range required by S. lalandi. Some zoonotic bacteria were found, as well as bacteria with probiotic and industrial uses. These results represent the first report on bacteriological quality in RAS for S. lalandi.