Gills are the main respiratory organ of aquatic animals. Different gill structures have existed in aquatic animals like fish, shrimp and crab, but they all hold similar functions in gas exchange, osmotic pressure regulation, etc. Currently, there is an increasing number of studies on functional genomics in gills of aquatic animals. The aim of this paper is to summarize the main findings on gill functional genomics in recent years, especially the transcriptome sequencing analysis of aquatic animal gills under the stress of different environmental factors, like pollutants of heavy metals, parasitic bacteria, salinity, nitrite, etc., as well as the proteomics and metabolomics of gills under the stress of different environmental factors. The study reveals the impacts of environmental factors on gill-related gene expression, physiological and biochemical status changes, molecular pathways and physiological functions in aquatic animals, so as to provide potential new ideas and directions for healthy fish farming.