Peace with the local Indians allowed St. Augustine to slowly develop into a small and prosperous town. However, in 1586, England and Spain were at war and the English corsair Sir Francis Drake was likely to attack on his way home. St. Augustine was fired upon on June 6. The English fleet was huge, forcing Governor Marquez and his people to flee. Immediately, Indians looted the town. When the English arrived, they took what the Indians left behind, and it is said the killing of an English soldier by the Spanish rearguard prompted Drake to issue his dreadful orders- "burn the town!"
As soon as Drake and his fleet set sail, Governor Marquez summoned help from Cuba. News of the disaster led to increased support in Spain for the struggling colony. St. Augustine was given the status of a “presidio” – a city that served as an official military fortress of the Spanish Empire. Soon after the residents of the abandoned Santa Elena arrived, the town of St. Augustine fulfilled one of its major roles – serving as a haven for the treasure fleets on their way home to Spain. Several ships loaded with treasure were wrecked on the Florida coast and the sailors were able to survive thanks to the food provided by the Indians.
When they weren’t converting Indians, rebuilding after storms or burying plague victims, St. Augustine’s residents were busy carrying out their duties to the Spanish crown. Its soldiers escorted missionaries and its sailors traveled frequently aboard ships sailing between St. Augustine and Havana. The town’s garrison was responsible for rescuing shipwrecked Spanish sailors and recovering the treasure and cannons aboard the ships run aground by storms or pirates. With a reputation as a savage wilderness, recruitment for the garrison sometimes took place in Spanish prisons. The viceroy was responsible for sending the annual "subsidy" or payment to the St. Augustine garrison, but in 1586, Sir Francis Drake helped himself to the town's finances. In 1627, the entire treasure fleet was captured by the Dutch corsair Piet Heyn. The subsidy for La Florida and all the presides in the Caribbean were lost. When funds were short, the capital of La Florida was short-changed on its annual paycheck. As a result, supplies from Havana and New Spain were essential for the town's survival.
It wasn’t long after Drake’s devastating raid that the residents of St. Augustine learned that other Englishmen had arrived in La Florida and this time they weren’t just conducting a raid, they were building a town. In 1607, the English returned and christened their new Virginia colony “Jamestown," after the inhabitants of their first settlement Roanoke (in present-day North Carolina) mysteriously disappeared.
In 1609 and 1611, scouting parties from St. Augustine revealed reports regarding the English intrusion into La Florida. During the mid-1600’s, roving bands of previously unknown Indian tribes, forced southward by the expanding English colony, began raiding Florida and murdering missionaries. St. Augustine’s pleas to strengthen the town’s garrison and fortifications went unanswered. In 1665, King Charles II of England announced that a new province named Carolina was to be created south of Virginia. The fact that the boundaries of Carolina included St. Augustine left no doubt about the ambitious extent of the English plans.
The English privateer Robert Sealers captured a Spanish ship headed for Cuba from Florida. He heard from a French doctor onboard that a large amount of silver was being stored in St. Augustine. Sealers sailed back up the coast of Florida in May of 1668. Waiting for nightfall, he brought the ship into St. Augustine’s harbor where its residents anticipated the arrival of this "supply ship" the next morning. After midnight, they went on a rampage through the town. The pirates helped themselves to the salvaged silver and ruthlessly murdered sixty residents of the town, including children. They ransomed off hostages and selected those Sealers judged to be not of "pure Spanish blood" to be sold into slavery elsewhere in the Caribbean. The Sealers Raid awakened the Spanish monarchy to the serious threat of the English colonies. In 1669, Queen Mariana ordered the Viceroy of Mexico to pay for the construction of a massive stone fortress to be as fortified as the most important cities of the Spanish Empire.
