Coral reefs are a source of marine diversity that must be protected, not only for the relationship between their ecosystem and other biota, but also for their economic value. Indonesia is an archipelagic country with 116 small islands and groups of small islands that are susceptible to ecological damage. Indonesia possesses a great diversity of flora and fauna, including coral reefs. Indonesia’s sea territory is twothirds the size of its land territory, and much of the nation’s ecological diversity lies within this water expanse. As coral reefs form a part of Indonesia’s marine diversity, we must protect them. This paper will discuss Indonesian regulations pertaining to the protection of coral reefs with a particular focus on Radja Ampat, Papua. The principal sources of relevant Indonesian statutory law are Law No. 23 Year 1997, regarding Environmental Management, and Law No. 5 Year 1990, regarding Biological Diversity and Ecosystems. These laws may be used to protect marine environments, especially coral reefs. At the international level, the United Nations Convention on the Law of the Sea and the Convention on Biological Diversity complement the laws enacted by Indonesia. Radja Ampat is located in Papua Province, and is known as a premier diving site. Surveys have brought Raja Ampat’s total number of confirmed species of coral to 537, representing an incredible 75% of all known coral species. Sadly, marine pollution in Radja Amapt is decreasing both the quality and quantity of coral reefs.