A protected area is defined by the Convention on Biological Diversity as "a geographically de-fined area, which is designated or regulated and managed to achieve specific conservation objectives".

Protected areas may be marine sanctuaries meant to protect biodiversity while serving other non-conflicting uses, or they may be areas set up to restrict or prohibit a particular activity, such as fishing or ship traffic, because the ecosystem is deemed to be particularly sensitive to that activity. Regulations depend on what are seen as the major threats to biodiversity and what the public will support or tolerate two criteria that may be in conflict with each other.

In multiple-use areas, exploitation of resources may be allowed within sanctuary boundaries; the challenge is to make sure the exploitation is restricted to sustainable levels. Large areas are usually preferable for multiple-use reserves, but their size makes enforcement difficult. Even in those rare areas with total, park-like protection, the effects of visitors must be mini-mised if protection is to work. Multiple-use marine protected areas are often seen as a vehicle for establishing effective integrated and adaptive management programmes.

Large areas are usually preferable for multiple-use reserves, but the large size makes en-forcement difficult. In order to be effective, people, especially potential encroachers, must be convinced that there is good reason to obey the restrictions. Therefore, education and raising awareness are the important parts of a protected area programme.

No-fishing areas are still astoundingly rare in the marine environment, are set aside to protect important spawning grounds or to provide a refuge area for species that are heavily fished in surrounding waters. Here, they have an opportunity to replenish their numbers and grow to a larger size, which benefits the fishery outside as well as the fish.

Despite the popularity of protected area approach in the national and international conservation community, these areas are not always defined and protected in a way that maximises benefits to the ecosystem. For instance, protected areas are often defined first by shoreline features or boundaries, then by bottom topography, and rarely by water circulation patterns. Yet, water circulation is probably the most important to pelagic communities and is critical to benthic communities as well.

Ten generally supported guidelines can be listed to guide the establishment or re-planning of protected areas that will have biodiversity conservation as their central or major purpose:

1. Number of areas.
   A large number of sites will provide better coverage of the diversity of habitats and transition areas in the country, and will better ensure against any catastrophic events or diseases.
2. Size.
   Ideally, each area should be as large as needed to embrace the biota of concern, together with the related habitats and ecosystem factors.
   
3. Interconnectedness.
   The intervening landscape or water areas should permit the flow of biota from site to site in response to daily and seasonal changes, climate change, and other large and small spatial and temporal-scale factors.
   
4. Zoning.
   Within the selected area, designation of various zones can segregate management objectives and uses that may be incompatible and identify management activities by area.
   
5. Location of facilities and infrastructure.
   Infrastructure can affect biodiversity. Therefore, even those limited facilities required by most protected areas, should be designed and located as part of the overall ecological assessment, mapping and analysis.
   
6. Research and monitoring programme.
   Management can be effective only to the extent that it is supported by information and knowl-edge.
   
7. Biological-resource management programme.
   Biological-resource management plan should foreseen and be prepared using vast array of methodologies for conserving biodiversity, based on the results of research and monitoring.
   
8. Education programmes.
   Protected areas are excellent places for educating people about nature and the relationship between nature and people.
   
9. Use management programmes.
   All IUCN management categories feature one or more types of human use, ranging from di-rect to indirect uses. The degree to which biodiversity can be conserved at the genetic, species and landscape/ecosystem levels will depend on how these use regimes are managed.
   
10. Bioregional management programmes.
    Protected area management where biodiversity is a major objective will succeed only to the extent that co-operative arrangements are made among public agencies, local residents and industry. These agreements must ensure that the management of biological resources and eco-systems in adjacent areas are consistent with the management objectives of the protected areas.