Sustainable development, in particular the implementation of the SDS-SEA, is a long-term endeavor. It requires an efficient regional coordinating mechanism that will place concerted efforts in developing, coordinating and nurturing the various efforts governments and stakeholder partners towards achieving the shared visions. The PEMSEA regional mechanism was established with the signing of the Haikou Partnership Agreement on 15 December 2006.

There are four major operating mechanisms: the East Asian Seas (EAS) Congress, the East Asian Seas (EAS) Partnership Council, the PEMSEA Resource Facility, and the Regional Partnership Fund.

• The East Asian Seas Congress
  
  Held every three years, the EAS Congress consists of a Ministerial Forum, an International Conference and other related activities.
  
  
• The East Asian Seas Partnership Council
  
  The EAS Partnership Council is a regular body composed of all Partners. The Council formulates both program and operational policy in support of the implementation of the SDS-SEA, based on policy direction, recommendations and commitments provided by the Ministerial Forum, EAS Congress, and other Partners.
  
  
• PEMSEA Resource Facility
  
  The PEMSEA Resource Facility (PRF) has two functions: (1) providing Secretariat Services; and (2) providing Technical Services.
  
  
• Regional Partnership Fund
  
  The Regional Partnership Fund, set up by the EAS Partnership Council, receives voluntary financial contributions from countries, international agencies, donors, institutions, individuals and any other entity for the implementation of the SDS-SEA.