Belize has an extensive barrier reef system extending for some 250 km along the entire coastline. The boundary for the Sapodilla Cayes Marine Reserve encompasses the southernmost section of the barrier reef. At this southern terminus the reef makes a J-shaped hook which is what makes up the Sapodilla Cayes Marine Reserve.  The eastern and western boundaries of the reserve follow the 100 meter depth contours along the reef. 

The reserve covers an approximate area of 119 km2 and includes twelve sand or mangrove cayes; namely, Northeast Sapodilla Caye, Frank's Cayes main, east and west, Nicholas Caye, Hunting Caye, Lime Caye, Ragged Caye, Seal Cayes I and II, and two unnamed sand cayes or ephemeral islands that are unvegetated and often overtopped by swash.

There are four different zones in place at the SCMR.  They include: preservation zone, conservation zone, general use zone and special management areas.  Each of these zones has different rules and regulations.

The goal of the preservation zone is: To provide areas within the reserve that are preserved in an entirely natural state; and to protect areas of particularly fragile habitat or with threatened or rare species.  Therefore this zone is under the strictest protection with no entry to visitors or researchers.

The goal of the conservation zone is: To provide an undisturbed area for recruitment of species to adjacent areas; to provide an area free from all fishing and collecting that will allow research and education; to provide a baseline to monitor the ecological status of unprotected areas; and to provide a representative sample of certain habitats within the protected area.  This is a controlled extraction zone to accommodate subsistence fishing, recreation and tourism.  This zone also enhances the fishery through controlled fishing.  There is no commercial fishing allowed in this zone however the area is open for non-extractive tourism purposes including, snorkeling, diving, kayaking, and sightseeing.  All anchoring within the conservation zone must be done on the designated mooring buoys.

The goal of the general use zone: To provide opportunities for established uses and activities (e.g. fishing for conch, lobster and finfish; recreational activities etc.) to be continued in a sustainable manner under a stringent monitoring scheme.  This zone lies apart from the more critical protection zones.  It is fairly accessible to local fishers as they presently use part of the area for commercial fishing. The existence of some fishing banks and nearby replenishment areas makes this zone a valuable and potentially fertile fishing grounds.

The goal of the special management areas:To provide