The first church on this site was probably built by Bodfan, a Celtic Saint, in the 6^th century. He no doubt built his church of wood and wattle but no trace remains of that building. Ancient maps refer to the church as St. Bodfan’s and an association with the Saint is preserved in the name of the nearby Bodfan farm but the church here today is more popularly known as St. Mary’s.

The present church was built about 1200 AD by Hywel ap Gruffudd ap Cynan, the Lord of Ardudwy. This Hywel was a near relative of Llewelyn the Great and great-grandson of Owain Gwynedd.

The present church was completely restored in the 1860’s as a result of the efforts of the Rev. John Jones, Rector of Llanaber from 1843 to 1887 and Mr. W.W. E. Wynne. The bell turret was re-built as well as most of the west wall with its heavy buttresses. The small vestry adjoining the north side of the Chancel was also constructed at the same time on the site of a previous building. Upon pulling down the west wall the upper part of an early coffin-lid was found embedded in the wall. This can now be seen just behind the font. In 1858 a bronze cross and early Crucifix figure was discovered among the remains of an altar, where the present organ now stands. It is kept at the National Museum of Wales in Cardiff.