In recent years, coral reef degradation has been increasing. Management and conservation efforts have tended to focus only on the physical condition of the coral reefs with less attention to biological and oceanographic aspects, in particular genetics and hydrodynamics. Genetic data can illustrate the connectivity between and within populations of an organism, making it is possible to determine source and sink populations or sites. Studies of physical water movements can also illustrate the likely patterns of movement or predict the mobility of coral planulae. Both of these approaches can help to strengthen Marine Protected Area (MPA) design, especially at the formation stage, in particular MPAs focused on coral reef ecosystems. Together, these two approaches can provide data on biological networks in a region and help delineate stocks. The implications of such studies can help to identify conservation priorities and improve the effectiveness of management processes in Indonesia, and can certainly enable the refinement of general approaches to help produce management plans tailored to local and regional conditions and processes. This brief review aims to review the constraints that occur in the management process, including barriers to and potential benefits of integrating molecular and hydrodynamic data into the management and conservation process, as illustrated through a critical review of MPA implementation in the waters around Sulawesi Island.
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