Large yellow croaker (Pseudosciaena croced) is an economically important marine fish in China suffering from severe outbreaks of infectious disease caused by marine bacteria such as Aeromonas hydrophila (A. Hydrophila), resulting in great economic losses. However, the mechanisms involved in immune response to bacterial infection are far from being fully understood. In order to understand the molecular mechanisms underlying the immune response to such pathogenic bacteria, we used high-throughput deep sequencing technology to investigate the transcriptome and comparative expression profiles of large yellow croaker infected with A. Hydrophila.