- Department of Innovative Technologies
- Remote Sensing Department
- Applied Sea Physics Laboratory
- Wave Theory Department
- Oceanography Department
- Shelf Hydrophysics Department
- Department of Dynamics of the Oceanic Processes
- Atmosphere and Ocean Interaction Department
- System Analysis Department
- Turbulence Department
- Marine Optics and Biophysics Department
- Marine Biogeochemistry Department
- Department of Marine Forecasts
- Department of Computational Technologies and Mathematical Modeling
- Center of Scientific Equipment test and application
- Experimental and mechanical laboratory
- Laboratory of interdisciplinary applied research and testing of marine robotic complexes
