Santa Maria was formerly a part of Guiling-guiling (now Siniloan) as a small village called Caboan.

Father Antonio de la Llave was assigned as the first parish priest of Caboan.

In 1602, the small village was converted into a town and renamed San Miguel de Caboan under the patronage of Saint Michael, the Archangel.

[1] Father Geronimo Vasquez built the stone church on the exact spot where the image of the Virgin Mary was found by a Caboan couple according to legend in 1613.

The church was destroyed by the 1639 Chinese uprising and was rebuilt in 1669 by José de Jesus María, as well as the rectory.