Conservation of biodiversity must take into account the full range of causes for its loss, and promote the opportunities that genes, species and ecosystems provide for sustainable development. Efforts for the conservation of biological diversity should ideally protect all levels in the hierarchy of biological diversity: genes, species, and ecosystems. The best way to maintain species is to maintain their habitats. The conservation of biological diversity therefore often involves efforts to prevent the degradation of key natural ecosystems and to manage and protect them effectively. Another component to the maintenance of biological diversity is restoring lost species to their habitats and restoring the habitats themselves. A part of this restoration may involve preserving species in genebanks, zoos, and other facilities.

Protection of critical habitats and ecosystems

The most effective mechanism for conserving biological diversity is to prevent the destruction or degradation of habitat. Habitat loss and modification is the principal factor in the decline of global biodiversity. On a regional level, 76% of all the species, which are in danger of extinction are threatened by habitat loss or habitat modification. The primary causes of habitat loss in the Wider Caribbean Region are human development for settlement, tourism, and agriculture, as well as forest clearance and pollution.

Monitoring habitats is fundamental to understanding the dynamics of biodiversity loss. Habitat monitoring includes several factors. These are recording changes in the geographical area of the habitat, recording changes in the condition or state of the habitat, and documenting habitat fragmentation. The problem of habitat monitoring is further complicated by the lack of an internationally accepted habitat or ecosystem classification system on a scale that is appropriate for national biodiversity management. Often, the classification system adopted is unique for the country, making regional and international comparisons difficult. There have been attempts to develop global biogeographic classification schemes, but these have been on large geographic scales and do not classify ecosystems on the scale that they are managed or monitored, such as coral reefs and seagrass beds. In addition, ecosystem mapping must take into account human impact on the landscape. Habitat maps should be used in conjunction with other environmental and natural resource maps in order to locate areas of interest for biodiversity ground surveys. Ecologically sensitive areas and habitats can be identified from a combination of existing maps and field surveys, and measures taken for their protection.

Protected areas and reserves provide a way to protect critical habitats and ecosystems, and can allow for the maintenance of representative samples of natural habitats and biological diversity. The Specially Protected Areas and Wildlife (SPAW) protocol of the Cartagena Convention provides for a network of protected areas to conserve and restore regional ecosystems, including specific components such as coral reefs, mangroves and seagrass beds. In almost every Caribbean nation a number of ecologically important areas have been designated by national legislation as marine and coastal parks and protected areas. Most marine protected areas in the Caribbean are not exclusively marine, but constitute an extension of coastal protected areas. In addition to establishing new marine protected areas, efforts and resources should focus on the management of those already established. The nature and effectiveness of protected area systems vary greatly from one country to another. In many cases the parks lack adequate control mechanisms, and are inadequately protected from mounting pressure on their space and resources. The size of protected areas varies, too. Small reserves can often protect a large number of species, although large reserves are required to support viable populations of species that have large home ranges.

Several regional initiatives to reduce environmental impacts on coastal ecosystems are either in place or under development. These include the Programme of Action for Sustainable Development of Small Island Development States, which adopted recommendations for implementing national, regional, and global mechanisms for the sustainable management and protection of coastal and marine resources and biological diversity. The Caribbean Environmental Network (CEN) Project, focusing on environmentally sustainable tourism, and the Land Based Sources of Marine Pollution Protocol, a part of the Cartagena Convention, are two examples of such mechanisms. On an international scale, the Ramsar Convention (Convention on Wetlands of International Importance) provides for strengthened protection of wetlands, including shallow coastal and marine areas. The Ramsar convention requires the acceding nation to designate at least one significant wetland site that is sustainably managed. This provides international recognition for the importance of the site and access to various forms of scientific and technical cooperation.

Restriction of commercial exploitation

Fisheries regulation requires international measures in addition to national legislation and enforcement. Many fish species have large ranges extending into several countries’ exclusive economic zones. Both UN Conference on the Law of the Sea, UNCLOS, and the FAO Code of Conduct for Responsible Fisheries emphasize regional cooperation as key to successful implementation.

International trade in endangered species is controlled by the CITES Convention. Some 118 countries are parties to the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). CITES regulates international trade of all species listed in its Appendices (I, II and III). Appendix I lists species threatened with extinction which are or may be affected by trade. Trade in these species is banned except in exceptional circumstances. Appendix II lists species not yet threatened with extinction, but which may become so unless their trade is subject to strict international controls. Appendix III lists species, which any party identifies as subject to regulation within its jurisdiction to prevent or restrict exploitation, and which require the cooperation of other CITES parties in the control of international trade.

The World Conservation Union (IUCN) assesses the conservation status of species worldwide and categorizes threatened species as endangered, vulnerable, rare, indeterminate, and insufficiently known. "Endangered" are those species that are in danger of extinction and whose survival is unlikely if the factors contributing to their condition persist. "Vulnerable" species are those which are believed likely to move into the "Endangered" category in the near future if the causal factors continue operating. Species, which have small populations worldwide that are not endangered or vulnerable, but are at risk, are grouped in the "Rare" category. The "Indeterminate" category contains species, which are known to be "Vulnerable" or "Rare" but where there is not enough information to say which of the three categories is appropriate. The "Insufficiently known" category contains taxa that are suspected but, because of lack of information, not definitely known to belong to one of the previous categories. The IUCN Red List of Threatened Animals contains listings of animals in all of these categories.

Control of genetic manipulation oc species and accidental introduction of alien species

Research in biotechnology based upon genetic resources is becoming more popular, and is an important area of research for biodiversity conservation. However, there are risks involved in using and releasing living, modified organisms. The Convention on Biological Diversity urges the contracting parties as a group to consider the need for a "biosafety" protocol. In addition, establishing a procedure where advanced information is given to a country on living modified organisms when transferred from one country to another. Each country has the right to refuse the importation of certain potentially hazardous materials. Information should be provided on the nature of the materials and the possible consequences of their release.

The United Nations Law of the Sea Convention (UNCLOS) Framework requires states to take measeures to control the accidental or intentional introduction of exotic species.

The possible consequences of building canals from one body of water to another one, which is not naturally in contact with the first, should also be considered. Many marine species in the Mediterranean have been introduced there through the Suez Canal. The introduced species include shrimps, fishes, and jellyfish, and they have had an effect of depressing the populations of ecologically similar native species.

The problem of release of marine organisms in ship ballast water continues without regulation in most areas, and will only stop when legislation prohibits the practice. Accidental introduction of alien species, with unpredictable consequences, will continue until effective national and international measures are in place.