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Glover's Reef Marine Reserve has been divided into four zones to allow for the management of resources for sustainability, to ensure the multiple uses of the marine protected area continue (Map). These range from the least regulated to the most restrictive:
- General Use Zone
- Seasonal Closure Zone
- Conservation Zone
- Wilderness Zone
A fifth zone has recently been created to offer greater protection to the north-east spawning aggregation site (see Northeast Point).
The Glover's Reef Marine Reserve encompasses the entire atoll, extending out to the 100-fathom depth contour, with a total area of 35,067 ha. To date, only the northern and western boundaries of the Conservation Zone have been demarcated by marker buoys.