For the Fisheries Commission to effectively and efficiently perform its mandate, it is organized internally into five (7) Divisions and three (3) special units, namely;
- Marine Fisheries Management Division (MFMD)
- Artisanal unit
- Industrial unit
- Inland Fisheries Management Division (IFMD)
- Freshwater unit
- Lagoon unit
- Mariculture unit
- Fisheries Scientific Survey Division (FSSD)
- Environment and Climate Change unit
- Fish stock and statistics unit
- Fishing gears and methods unit
- Monitoring, Control, and Surveillance Division (MCSD)
- Fisheries monitoring centre unit
- Fisheries enforcement unit
- Inspections unit
- Finance and Administration Division (F&A)
- Human Resource unit
- Corporate Affairs unit
- Information Technology unit
- Procurement unit
- General Administration unit
- Planning, Budget, Monitoring and Evaluation Division (PBMED)
- Planning unit
- Budget unit
- Monitoring and Evaluation unit
- Post-Harvest Management and Trade Division (PHMTD)
- Post-Harvest Management unit
- Fish Trade unit
SPECIAL UNITS
- Legal and Compliance unit
- Aquatic Animal Health unit
- Internal Audit unit