Salinity is an important abiotic stress, has significant effect on the physiological and metabolism activities, reproduction, growth, survival and development of marine fish. The greater amberjack (Seriola dumerili) is a large, fast-growing species with high commercial value in aquaculture worldwide. We performed RNA-seq analysis of the brain to identify the genes and molecular biological processes involved in response to salinity changes. The candidate genes identified in this study provide a basis for further research on the molecular mechanisms of salinity adaptation and transcriptional plasticity of marine fish.