With the growing demand for animal protein, aquaculture plays a major role in sustaining proteins despite many challenges like disease outbreaks, lack of genetic resources, and environmental impacts. Omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and multi-omics, are used to overcome these issues and increase food security. Each omics technology contributes unique insights that, when combined, enhance our knowledge of complex biological systems and improve aquaculture practices. Transcriptomics deals with RNA transcripts, which are crucial in understanding their gene expression in response to intrinsic and extrinsic factors like abiotic stress, diseases, growth, temperature, and other environmental factors. This transcriptome data can help us analyze and identify various biomarkers, like growth optimization markers and markers related to reproductive traits, and it will also help develop disease-resistant strains. Moreover, it also acts as a molecular basis for understanding the environment’s adaptability and helps reveal the complex relationship between host and pathogen. So, this multidimensional cognition is required to enhance the health, resilience, and productivity of economically important candidate fish species, making the aquaculture sector a more sustainable future. Integrating transcriptomics with other omics techniques offers promising solutions for sustainable aquaculture, improving productivity, health, and environmental sustainability.