Institut Penyelidikan Marin Borneo telah menerima beberapa pengiktirafan diperingkat nasional dan antarabangsa.

Antara yang terkenal ialah:

• Potential Higher Institutional Centre of Excellence (HICoE) in Aquaculture, Ministry of Education Malaysia
• International Ocean Institute’s Focal Point for Malaysia
• Network membership of The Ocean Project
• Membership of International Maritime Club and
• Centre for collaborative research in aquaculture by Kinki University, Japan.