The identification of key genes that are involved in the response to stressors is crucial for controlling stress in fish species and sustainable aquaculture. Environmental stressors can induce stress responses in aquatic animals, resulting in compromised immune function, inhibited growth, and increased mortality rates. mRNA-seq analysis provides a powerful tool to identify key genes and pathways associated with the stress response. In the present study, mRNA-seq analysis was employed to identify key overlapping differentially expressed genes (DEGs) and molecular pathways under multiple stressors (salinity, nitrite, copper, and pH stress) in Nile tilapia (Oreochromis niloticus).