The place has been known as Santoña since before it was conquered by the Romans. The name of the town is derived from the Santones or Sántonos tribe, who may have had Celtic roots. But like so many other Cantabrian towns, Santoña owes it origins to the repopulation ordered by Alfonso I the Catholic, King of Asturias, in the 8th century. A century later, a settlement sprang up around the Monastery of Santa María de Puerto, which had authority over the port and its territory. In fact, old documents distinguished between Santoña (the area around the hills) and “El Puerto” (the village surrounding the old monastery).
In 1038, Santoña continued to grow in importance and population thanks to Abbot Paterno, who is considered the true founder of the city by many historians. In the 12th century, the Monastery of Santa María began to lose its power when it came under the authority of the Nájera Abbey. The aristocracy and abbot of Santoña fought to break away from Nájera. This separation finally took place in 1579, when Santoña became a villa de realengo (town under direct control of the monarchy) and was absorbed into the Juntas of Trasmiera. At that time it came to be known as Puerto de Santoña, and this name was maintained until the 18th century when it was shortened to the present-day name of Santoña.
Due to continuous attacks by the French, particularly the 1639 siege ordered by the archbishop of Bordeaux, two defensive forts were built in Santoña: San Martín Fort and San Carlos Fort. Years later, the French themselvesmade the town a French stronghold during the Peninsular War and built two new forts there: the Imperial Fort (on the site of the present-day El Dueso Penitentiary) and Mazo Fort.
In the late 19th century, Santoña’s commercial port was built, attracting Italian industrialists who would purchase cured anchovies for use in their own country. World War I had a great impact on this industry’s exports. In 1915, during the war, an Italian came up with a solution to this issue and started cutting the anchovies into fillets and packaging them in cans, in accordance with the preservation process that is used today. At that time many Italians began to migrate to Santoña, spurring the growth of its canned anchovy and tuna industry, one of the most important canned fish industries in the world.