Global awareness is rising regarding the health implications of global climate change and environmental pollutants, which are hazardous to both human and animal welfare. Teleost fish are known to be highly sensitive to the hazards caused by human activity and changes in the surrounding ambient environment, and they are commonly used as a biomonitoring species in the aquatic environment. Transcriptomic analysis has recently been widely performed to determine the relationship between the physiological activity and molecular biological alteration of teleost fish under environmental stress. MicroRNAs (miRNAs) are highly conserved and small non-coding RNA molecules that participate positively with increased variety of biological activities through the post-transcriptional organization of gene expression. The discovery of these molecular pathways will contribute to a better understanding of detoxification processes, resistance to disease outbreaks, and ecological stresses, as well as provide important tools for predicting the risk of environmental pollutants. In the current review article, we summarized the miRNA modulating role against several types of environmental stressors (thermal, hypoxia, salinity, pollutants and diseases). In addition, we presented a comprehensive horizontal summary of major findings and discussed recent applied strategies for miRNA manipulation in aquaculture, with an emphasis on future research directions.