San Pedro de Alcantara was inhabited by the Romans as shown by the ruins of La Bovedas, and this dates to the 3rd Century AD. There was the Basilica of Vega del Mar from the 4th Century and the watch tower from the 16th century.
In 1858 General Manuel Gutierrez de la Concha, the first Marques del Duero, arrived in the municipal and started a farm and called it the Colonia Agricola de San Pedro Alcantara. The company was so named to honor his mother, Petra de Alcantara Irigoyen y de la Quintana, and San Pedro Alcantara, the saint from Extremadura that his family was devoted to.
He built a system of small dams to permit irrigation of about 10,000 hectares. He bought the latest agricultural machines from the US and Britain. He imported experienced agricultural workers from Granada, Almeria, Valencia and Murcia. He offered the workers a home and a small plot of land adjacent to the home to grow vegetables for the family. He started a school of agricultural experts, the first in Spain. He also ordered the construction of roads for communication, some of them still in use today. He constructed shipping facilities to send his sugar cane to Malaga.
The Marques constructed the town with straight streets and perpendicular streets between 1860 and 1870, with the center at the church plaza.
Unfortunately the farm could not pay for all the debts that the Marques had incurred when he started the farm and he and his daughter had to sell the farm in 1874. The farm continued functioning, growing sugar cane, until 1920.
The town built a statue to the Marques del Duero in 1995 at the town plaza. The sculptor was Santiago de Santiago.