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Through the years, MSI has made a significant international contribution to tropical marine science. In the last thirty-eight years (1974-2012), MSI generated over 500+ ISI publications, and hundreds of papers in national and international proceedings, and local journals combined. In addition, MSI has produced numerous books, manuals, and field guides. At the national level, these contributions form the bases of policies that guide the research and development programs of the country. MSI scientists have also made significant contributions to the formulation of international policy on the environment through their participation in various programmes and activities of the United Nations system.

Among the ranks of the MSI faculty are two National Scientists, several Academicians and Corresponding members of the National Academy of Science and Technology (NAST), several Outstanding Young Scientists, a NAST-Third World Academy of Science Awardee, several Hugh Greenwood Environmental Awardees (NAST), and a number of outstanding national and international individual awardees.

In recognition of its achievements in research and instruction, the Institute has received numerous awards from both government and private organizations both locally and abroad. On 15 December 1994, MSI was designated the “National Center of Excellence in Marine Sciences” by Presidential Proclamation No. 518. In 1998, the Commission on Higher Education (CHED) declared it the first Center of Excellence for Marine Sciences. MSI is also the regional Center of Excellence of the Global Environment Facility-Coral Reef Targeted Research programme for Southeast Asia. In July 2008, MSI was co-awardee of the prestigious Calouste Gulbenkian International Prize for its work on biodiversity and defense of the environment.