Although both towns are pronounced Llanfaes in Welsh, the British government distinguishes an identically named settlement in Glamorgan by spelling it Llanmaes.

In the medieval kingdom of Gwynedd, Llanfaes functioned as the royal demesne (Welsh: maerdref) and seat of local governance for the commote of Dindaethwy in cantref Rhosyr[2] King Cynan Dindaethwy maintained his royal court (Welsh: llys) in the town around the turn of the 9th century, but he was killed amid a protracted struggle against a rival named Hywel.

The Llanmaes suffered during the rebellion of Madog ap Llywelyn (1294–95),[8] at the end of which Edward I visited Llanfaes and ordered the construction of the new castle and town of Beaumaris nearby as part of his pacification campaign.

The nearby site of Porth y Wygyr ("Vikingport") or Cerrig y Gwyddyl ("Irishstone") was chosen and Edward evicted Llanmaes's Welsh population to the opposite coast of the island, turning Rhosyr into "Newborough".

The monastery at Llanfaes was restored with help from Edward II (r. 1307–27) but then thoroughly plundered and destroyed by agents of Henry IV as a punishment for its friars' support of the Glyndŵr Rising (1400–1415).

[11] The fortress first established by the Normans was held during the English Civil War by Sir Thomas Cheadle on behalf of the Parliament, but was taken from him by Col. John Robinson in 1645 or '46.