Cod larvae were reared with two different rearing water systems: a recirculating aquaculture system (RAS) and a flow-through system (FTS). Four replicate tanks were used for each system. RNA extracted from individual larvae at 8, 13, and 17 days post hatching was used for microbiota characterization. Bacterial cDNA was synthesized and used for 16S rRNA PCR, followed by 454 pyrosequencing.