The ancient name of Llanfaes was Llan Ffagan Fach in honour of Ffagan, the founder of the church. It was once the royal court (llys) of King Cynan Dindaethwy ap Rhodri of Gwynedd (who reigned 798 – 816), the seat of the commote of Tindaethwy in the cantref of Rhosyr.
The site gained its present name as the site of a battle in 818, the Battle of Llanfaes, fought between unidentified combatants.[note 1]
A Franciscan monastery was founded here by Llywelyn ap Iorwerth, built over the grave of his wife Joan, daughter of King John, who died in 1237. Wasted in the aftermath of Llywelyn's fall in 1240, it was somewhat restored with help from Edward II (reigned 1307 – 1327), but was thoroughly plundered and utterly destroyed by the men of Henry IV due to the adherence of the friars to Owain Glyndŵr in his rising of 1400 – 1415. Following a recovery, whatever remained was finally diminished by the Dissolution in 1537, with the church then turned into a barn, and Joan's stone coffin used as a watering trough.
- Various sources assume that there was an invasion by the Mercians, by Egbert of Wessex, or by the Vikings, but there is no authority for any of these assertions. It might also have been a recurrence of the dynastic strife between Gwynedd's Cynan and Hywel (reigned 816 – 825) that had raged for several years on Anglesey, from 812 onward.
- Morgan, Thomas (1887), "Llanfaes", Handbook of the Origin of Place-names in Wales and Monmouthshire, Merthyr Tydfil: Thomas Morgan, p. 138
- John Edward Lloyd (1911), "The Tribal Divisions in Wales", A History of Wales from the Earliest Times to the Edwardian Conquest, I (Second ed.), London: Longmans, Green, and Co. (published 1912), p. 232
- Parry, Henry (translator), ed. (1829), "Brut y Saeson", Archaeologia Cambrensis, Third, IX, London: J. Russell Smith (published 1863), p. 63, http://books.google.com/books?id=28A1AAAAMAAJ&pg=PA63
- Hughes, William (1911), "Appendix D", Diocesan Histories: Bangor, London: Society for Promoting Christian Knowledge, pp. 187 – 188