The site is older than the present building. A clas settlement - a community of Celtic Christian monks - was established here in the 5th to 7th centuries by St Hywyn, an early Welsh saint who had come from Brittany. The clas would have been a wooden enclosure with a small stone chapel and a scatter of cells - the kind of foundation that produced the early saints of Wales. Some of those saints went on to Bardsey to be buried. Some stayed in Aberdaron and became part of the local cult. By the 11th century, when the church first appears in written records (1115), it had become a stone-built parish church serving both the local community and the through-traffic of pilgrims heading for the abbey across the sound.

The most striking architectural feature of St Hywyn's is that it has two naves of equal length, joined by an internal arcade. The northern nave is largely 12th-century. The southern nave was added in the 14th or 15th century, almost certainly to accommodate the increasing flow of pilgrims after the 1119 papal declaration that gave Bardsey its full status as a pilgrimage destination. The church suddenly needed twice the floor space - so they built a second nave alongside the first and connected them through pointed arches. The result is a twin-aisled building, low and broad, sitting parallel to the shore. The building is constructed of rubble stone with slate roofs and a small bellcote. The internal arcade dates to the 15th century. The whole thing is Grade I listed - the highest grade of architectural protection in Wales.

The Reformation in the 16th century was the beginning of a long decline for the church. Pilgrimages stopped. The Catholic infrastructure that had supported the abbey on Bardsey was dismantled by Henry VIII's commissioners in 1537. St Hywyn's lost its purpose as a pilgrim staging-post and became simply the parish church of a remote and shrinking village. By the 19th century the building was in serious disrepair. In the 1850s, the parish built a new church inland - Eglwys Newydd, the New Church - intending to abandon the seaside building. The new church proved deeply unpopular with the congregation. They wanted their old church back. Eventually St Hywyn's was restored, and Eglwys Newydd became the redundant building instead. The locals had been right. The setting matters.

From 1967 to 1978, the vicar of St Hywyn's was R.S. Thomas - one of the great Welsh poets of the 20th century. He was nominated for the Nobel Prize in Literature in 1996. He had learned Welsh as an adult and become an ardent Welsh nationalist. His poetry, which a number of critics consider the finest religious verse of his generation, was rooted in landscape and the difficult, sometimes silent presence of God in remote places. Aberdaron, at the end of the road on the end of the peninsula, was the appropriate parish for the man and his work. After he retired he stayed in the area, living for some years in Y Rhiw. The church holds an annual festival in his memory each June, devoted to his work and that of his wife, the painter Mildred Eldridge. The church itself remains active, part of the Bro Enlli Ministry Area. Bro Enlli - the country of Bardsey. The name preserves the connection. The boats still cross the sound when the wind allows.