The research programmes of the fisheries research institutes have been strengthened, re-structured, re-oriented and prioritized with thrust on enhancing fish production and productivity through optimum and sustainable utilization of resources with due emphasis on conservation of fish resources to realize the full production potential from the fisheries and aquaculture sectors and to address the critical research gaps. The research implementation, monitoring and evaluation mechanism has also been strengthened for bringing more accountability and transparency in the research programme.

• Development and up-gradation of databases of finfish, crustaceans, molluscs and other important aquatic organisms, including their molecular aspects.
• Mapping potential fishery resources of the country using geo-spatial data and remote sensing for generating computer-based models for management of fishery and aquaculture resource management. 
• Development of sustainable management models for open-water fisheries resources in the context of changing resource structure and climatic conditions.
• Developing/upscaling of breeding and seed production technologies of important species of freshwater, brackishwater and marine ecosystems for commercial and conservational uses.
• Species and system diversification of commercially important fish species for freshwater, brackishwater and marine aquaculture.
• Climate change resilience, and adaptation and mitigation strategies. 
• Genetic improvement of commercially-important finfish and shellfish species for growth, disease resistance and other important traits through selective breeding and marker-assisted selection.
• Breeding and rearing of ornamental finfishes and shellfishes of freshwater and marine origin.
• Development of cost-effective and nutritive diets for different life stages of diversified fish and shellfish species, including ornamental species.
• Development of diagnostics, vaccines and disease management measures for current and emerging diseases. 
• Undertaking aquatic animal disease surveillance for preparedness against disease outbreak.
• Surveillance of antimicrobial resistance in different aquaculture systems.  
• Development of genomic resources for important fish and shellfish species through whole genome sequencing and transcriptome analysis.
• Development of eco-friendly fishing craft and gear for responsible fisheries.
• Post-harvest value addition and development of industrial/pharmaceutical products from fish and fish wastes.
• Reduction of harvest and post-harvest losses of fish through mitigation measures. 
• Development of fish farming technology for inland saline and sodic areas.
• Human resource development through higher education and training in different aspects of fisheries and aquaculture.
• Policy advisory for addressing various issues of fisheries and aquaculture.