Since the demand for seafood products is growing and aquaculture provides more than fifty percent of the aquatic food as reported by FAO, the development of more accurate and sensitive analytical techniques in order to screen and evaluate the safety and quality of seafood products is needed. At this point, several omic techniques like proteomics, lipidomics, and metabolomics, or combinations of them, are used for integration into seafood processing and quality control. Moreover, according to the literature, using the respective techniques can prevent, control, and treat diseases in fish as well as address several issues in aquaculture. Proteomic techniques are used for the expression of proteins and their modifications. Metabolomic techniques are used for accurate identification of species, while lipidomics techniques are used for the identification of different or specific lipid molecules in fish species, as well as fatty acid composition and location distribution. This review is to cover the recent proteomics, metabolomics, and lipidomics studies on aquatic and seafood products in the areas of quality, safety, processing, and breeding of fish.