In November 1996, divers with the private research firm, Intersal, Inc. discovered a room-sized mound of cannons, anchors, and ballast stones. Eight years earlier, in 1988, Intersal had received a permit from the North Carolina Underwater Archaeology Branch, (UAB) to search for the remains of Queen Anne's Revenge and its sloop, Adventure, in Beaufort Inlet. Intersal also held a permit to search the same area for the Spanish ship El Salvador, lost in 1750.

For nearly 10 years, Intersal conducted intermittent surveys in Beaufort Inlet with little result. Then, in 1996, Intersal hired shipwreck researcher Mike Daniel to direct field operations. Using historical accounts provided by Intersal President, Phil Masters, Daniel selected a survey area that he felt encompassed the inlet's early-eighteenth century entrance channel and bar. At the time of discovery, the Intersal crew recovered several artifacts dating to the early-eighteenth century including a brass blunderbuss barrel and a bronze bell with a date of 1705.

After a brief site visit and an inspection of the small collection of recovered artifacts, state underwater archaeologists agreed that the site was quite possibly the remains of Blackbeard's flagship, Queen Anne's Revenge. Fieldwork thus began in the fall of 1997. It was to be the most ambitious archaeological assessment of a North Carolina shipwreck since the discovery of the Civil War ironclad USS Monitor three decades earlier.

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