There is a growing interest for the progress and application of transcriptomics technology in recent years.Two types of techniques, including hybridization-or sequence-based method, have been developed for transcriptome investigations.With the emergence of next-generation sequencing techniques, those technologies have been widely used in the genetic studies of economic traits and molecular-aided selections for aquatic animals.This review has briefly summarized the progress of transcriptomic researches in aquaculture, involving immune response, growth, development, evolution and toxicology.Meanwhile, we have discussed challenges in both transcriptomic technologies and elaborate applications in aquaculture and analyzed prospects of further development of transcriptome researches on aquatic animals.