Descended from domesticated Spanish horses and possibly brought to the Americas in the 16th century, the ancestral foundation bloodstock may have become feral after surviving shipwrecks or being abandoned on the islands by one of the exploratory expeditions led by Lucas Vázquez de Ayllón or Sir Richard Grenville.

Bankers are allowed to remain on the islands due to their historical significance even though they can trample plants and ground-nesting animals and are not considered to be indigenous.

To prevent overpopulation and inbreeding, and to protect their habitat from being overgrazed, the horses are managed by the National Park Service, the state of North Carolina, and several private organizations.

The presence of the genetic marker "Q-ac" suggests that the horses share common ancestry with two other breeds of Spanish descent, the Pryor Mountain Mustang and Paso Fino.

[9] The breed shares skeletal traits of other Colonial Spanish horses: the wings of the atlas are lobed, rather than semicircular; and they are short-backed, with some individuals possessing five instead of six lumbar vertebrae.

Ships returning to Spain from the Americas often took advantage of both the Gulf Stream and continental trade winds, on a route that brought them within 20 miles (32 km) of the Outer Banks.

[11] Another conjecture is that the breed is descended from the 89 horses brought to the islands in 1526 by Spanish explorer Lucas Vázquez de Ayllón.

Lacking effective leadership, the new settlement lasted for only two months; the survivors abandoned the colony and fled to Hispaniola, leaving their horses behind.

[12] A similar theory is that Sir Richard Grenville brought horses to the islands in 1585 during an attempt to establish an English naval base.

[13] Documents indicate that the ships carried various types of livestock obtained through trade in Hispaniola, including "mares, kyne [cattle], buls, goates, swine [and] sheep.

Scholars believe that as the crew attempted to lighten the ship, they either unloaded the horses or forced them overboard, letting them swim to shore.

[18] Domesticated Bankers raised on manufactured horse feed from an early age tend to exhibit slightly larger frames.

[20] The National Park Service (NPS) is concerned about the impact of Bankers on the environmental health of North Carolina's barrier islands.

Initially, the NPS believed that the non-native Bankers would completely consume the Spartina alterniflora grasses and the maritime forests, as both were thought to be essential to their survival.

[23] To cope with the expanding population, prevent inbreeding and attempt to minimize environmental damage, several organizations partner in managing the herds.

Population management is achieved through adoption and by administering the contraceptive vaccine Porcine zona pellucida (PZP) to individual mares via dart.

The identification of individuals allows the National Park Service to ensure correct gender ratios and to select which mares to inject with PZP.

[26] On November 12, 1996, the Shackleford horses were rounded up by the North Carolina Department of Agriculture's Veterinary Division and tested for equine infectious anemia (EIA).

Finding a permanent, isolated area for such a large number of Bankers was a challenging task for the Foundation; eight days later the state declared all proposed locations for the herd unsuitable.

As a result of its efforts, the remainder of the herd was moved to a more remote part of Currituck Banks,[31] where they were fenced into 1,800 acres (7.28 km2; 2.81 sq mi) of combined federal and privately donated land between Corolla and the Virginia/North Carolina line.

[34] A herd lives on the Rachel Carson component of the North Carolina National Estuarine Research Reserve, a series of five small islands and several salt marshes.

Malnourishment caused by overcrowding resulted in the deaths of several horses; the reserve's staff instituted a birth control program to restrict the herd to about 40 animals.