In the early 13th century, Oton was already a flourishing Malay settlement. Its port, now a site of Batiano Bridge,was one of the five ancient Malay ports in Irong-irong trading with the Sanglays (Chinese merchants). Other inter-island ports were Sugbu, Madiano, and Malandog.

Oton became a seat of the Madia-as Confederation (Katiringban et Madia-as) in Panay under Datu Piburong until 226 A.D. The seat of the confederation was in Katagman (now Brgy. San Antonio), a nose shaped island surrounded by Batiano river where Irong-irong, later Iloilo got its name.

In 1556, the famous cosmographer and mathematician Fray Martin de Rada, O.S.A. one of the religious expedition of Legaspi and known to Augustinian historians as the Founder of Oton, came from Cebu and preached the Christian doctrine along the Batiano River.

Oton is a hispanized version of the phrase “Ogotong Adlaw”. When Spanish explorers asked a native about the time of the place, the latter answered ogtong adlaw (noontime) thinking that the Spaniards were asking about the time of the day.

In 1556, Father Martin de Rada made Oton as a strategic hiding place for Miguel Lopez de Legaspi and his armada from the Portuguese squadron. The fortification was built by Captain Diego de Artieda Chirino. In the same year, Adelantado Legaspi divided the colony into encomiendas, and appointed Don Miguel de Loarca as encomendero of Oton. Legaspi stayed in Oton before conquering Manila and Cavite. Father Rada, first Provincial islands, built in Oton the first church in the country in honor of our Lady of the Immaculate Conception in 1570. It was located at the tip of the Batiano River, now the site of the present Catholic Church and Convent.

During the Chapter Assembly of the Province of the Most Holy Name of Jesus in the Philippine Islands on May 3, 1572, Fr. Martin de Rada officialy signed the acceptance of Oton as Pueblo and the house of the Order. It became third in the country after Manila and Cebu. It was a big pueblo which includes the present towns of Alimodian, Leon, San Miguel, and part of Cabatuan.

In the same year, the Pueblo of Oton was made capital of the Province of Oton (La Alcadia de Oton) which covers the islands of Panay, Tablas, Sibuyan, Guimaras, Romblon and part of Negros.

Oton has also the distinction as the place where the first council of the Church of the Philippines was first convened to decide and answer questions on matters of social justice.