This article reviews the governance and management of Marine Protected Areas (MPAs), and the coral reefs they contain, in the eastern African Region. This includes the Comoros, Kenya, Madagascar, Mauritius, Mozambique, Tanzania, and the Seychelles. Three generations or categories of MPAs are distinguished: i) small areas for protection of a single species or unique marine habitat; ii) large multiple use MPAs designed for coastal development as well as biodiversity protection; and iii) MPAs managed by a nongovernmental organization (NGO) or the private sector. Each of these MPA types is examined according to the policies, legislation, and management systems they entail as well as the economic and community situation they operate within. The paper also provides a review of some eastern African MPAs in terms of their size and location, the type of MPA, zonation schemes, and financial status. The successes of the different types of MPAs are discussed based on specific indicators, such as changes in biodiversity, infrastructure, compliance to regulations and the level of involvement of primary stakeholders in the management. From the review it is clear that a fourth generation of MPAs may be forthcoming; community-based MPAs. Although lack of data makes it difficult to assess the effectiveness of these different categories of MPAs, it is clear that no MPA can succeed without support of the local communities. Generally, the results of the analysis are promising for MPAs, however a lack of data is hampering a deeper analysis. The major issues facing MPAs in the region are highlighted, as well as some regional initiatives striving to address these issues. A number of recommendations are made, aiming to strengthen the establishment and management of MPAs in the eastern African region.