Background: Shrimp farming is evolving from semi-intensive to hyper-intensive systems with biofloc technology and water recirculation systems. Objective: To evaluate the transcriptional response promoted by biofloc on shrimp (Litopenaeus vannamei) under a recirculating aquaculture system (RAS). Methods: Quantitative real-time RT-PCR was used to monitor seven key genes related to the immune system in shrimp post-larvae, reared in a RAS with and without biofloc (BF and no-BF). In addition, we present for the first time nucleotide sequences of ADP-ribosylation factor 4 (LvArf4) from Litopenaeus vannamei. Results: Transcripts for penaeidin3 (Pen3), penaeidin4 (Pen4), crustin, and Toll receptor (LvToll) genes were up-regulated between 3 and 24 h in both systems, and tumor necrosis factor receptor-associated factor 6 (TRAF6) in no-BF as an early response. Regarding differential expression between treatments, 13 occurrences were encountered. Nine that were higher in BF than in no-BF and four higher in no-BF than in BF. In some sample times, expression of Pen3, crustin, LvToll, TRAF6, IMD, and LvArf4 was higher in BF than in no-BF and in others, expression of Pen3, Pen4, and TRAF6 was higher in no-BF than in BF. Conclusions: BF modulates the transcription of genes related to the immune response in shrimp as an early response. However, the RAS with no-BF promotes a similar response.