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The J.N. "Ding" Darling National Wildlife Refuge is managed as part of the J.N. "Ding" Darling National Wildlife Refuge Complex. A National Wildlife Refuge Complex is an administrative grouping of two or more refuges, wildlife management areas or other refuge conservation areas that are primarily managed from a central office location. Some Refuges are grouped into a refuge complex structure where they occur in a similar ecological region, such as a watershed or ecosystem, and have related purposes and management goals.  Typically, a project leader oversees the general management of all refuges within the complex and refuge managers are responsible for operations at specific refuges. Supporting staff, composed of administrative, law enforcement, biological, fire, visitor services, and maintenance professionals, typically are centrally located and support all refuges within the complex.

The J.N. "Ding" Darling National Wildlife Refuge is part of a larger complex that encompasses the Caloosahatchee National Wildlife Refuge, The Matlacha Pass National Wildlife Refuge, Pine Island National Wildlife Refuge, and Island Bay National Wildlife Refuge. The majority of the lands in these refuges are nesting and roosting islands. The entire complex is approximately 8,000 acres. The Refuge Complex headquarters is located at 1 Wildlife Drive, Sanibel, FL 33957.