The Aber Valley has a history going back at least 4,000 years. It has been the site of early industry and of the court of royal princes. Some of that history is described on displays located in Tŷ Pwmp, close to the entrance to the village.
The centre of the village contains a small flat-topped motte, probably built by the Normans during one of their incursions along the north coast. The ditch around the motte is almost filled in and there is no sign of a bailey. Excavations of the adjoining field, carried out by the Gwynedd Archaeological Trust in 1994 revealed the stone foundations of a substantial winged hall, along with mid-13th century pottery.
Abergwyngregyn is known from historical documents to have been the site of one of the principal courts of the princes of Gwynedd. The exact location of the Llys is unknown. Some favour a siting at Pen y Bryn, on the other side of the river, but the recent archaeological evidence supports antiquarian tradition that the Llys was adjacent to the motte. Llywelyn ap Iorwerth is said to have preferred his Llys here to the more ancient site at Aberffraw on Anglesey. His wife Siwan died here in 1237, as did their son Dafydd in 1246. The village has been home to a mill for hundreds of years, possibly going back to the time of the Welsh Princes. The current mill is located in the centre of the village and was enlarged or rebuilt in the mid-19th century, probably after the Penrhyn Estate acquired the Manor of Aber from the Bulkeley Estate of Baron Hill, Beaumaris. It was used as a flour mill, and went out of use before the 1st World War. The mill was offered for sale in the Penrhyn Estate sale of 1925 (to pay for death duties), but failed to sell at the time. Later it was gifted to “The Young Men of Aber” for community use in the 1930’s and has more recently been renovated for community use.