Villasis was a mere barrio of Malasiqui in the early part of 17th century and was known by its name Pandoyocan. The place had no fixed boundaries. It was simply a frontier settlement, a thickly forested region covering most of the southeastern part of the province. Few people lived in this place due to unavailability of open spaces for farming. Its thick forest however was a nesting ground of bees called oyocan. The abundance of honey attracted Spaniards and inhabitants of neighboring places to settle in this village. From this, the place was made popular by tits great hordes of bees and they called the pace Pandoyocan meaning colony of bees.

The friars in Malasiqui undertook the task of converting the settlers in and around Pandoyocan persuading them to settle in a proposed pueblo. It was upon the petition of Fr. Fernando Sta. Maria, then assigned to Malasiqui, together with the principales of thetown the license to found the town of Pandoyocan was granted on October 18, 1759 by Bishop Miguel Espelita of Cebu, then the interim Governor General. He was the first Filipino Archbishop and Governor General. In 1769, it was placed under the care of the vicar of Sinapog known today as the town of Asingan.

Pandoyocan, had its first election of town officials in 1760. But during the Palaris Revolt of 1762-1764 its inhabitants dwindled to compose only 150 tributes and its administration was ordered abolished. Conceivably, the old residents stayed on and eventually it population increased.

Migrants from the Ilocos towards the end of the eighteenth century and the beginning of the nineteenth century further increased its population and the inhabitants petitioned for the restoration of their municipality. On the 22nd of June 1804 a royal decree was published mandating, the reconstitution of Pandoyocan. There was some delay in the execution of the decree and the inhabitants made another petition to re-establish their own government and at the same time to change the name of their town to Villasis in the honor of the former Governor Jose Maria Aguilar, one of whose family names was Villasis, who had issued the decree of 1804. Governor Felgueras granted the petition and the decree of 1804 was amended to name the town Villasis.