The original name of the town, Cabalian, was what the Spaniards knew.
When Legaspi visited Cabalian forty years after Magellan in 1561, they found the natives unfriendly and this discouraged the Spaniards. Legend has it that Magellan tried to anchor in the place due to a broken mast and shouts from the natives “kabalian”(meaning broked) were taken by the Spaniards to be the name of the place. No historical basis existed however. Pigafetta’s diary never mentioned the incident.
Excavated relics have shown that since the later part of the 13th century the town was known as Cabalian. The Jesuits in 1620 had buildings constructed and a watchtower build armed with faconetes y bantakas(Light cannons).
The change of the names from Cabalian to San Juan was made in honor of the towns patron saint. Saint John the Baptist. The town has 18 barangays.