Several visitors in the early part of the twentieth century noted that there were a variety of ancient remains on the island, but no serious studies were made until the 1960s.

Many earth structures have been identified, some of which may date back two or three thousand years. They consist of round huts and rectangular structures and are situated mostly on a small sheltered terrace on the mountain or in groups at Penrhyn Gogor at the northern end of the island. The latter are thought to be agricultural buildings dating from the middle ages.

The thirteenth century Abbey tower is the most prominent ancient monument on the island. A carved stone, bearing an inscription and dating from the ninth century, can be seen in the chapel. Many burial sites have been found in the vicinity of the Abbey, giving some credence to legend that the island was the burial place of twenty thousand saints, although the number is surely exaggerated.

Near the site of the present track, it is also possible to see ruins of former farmhouses. One of these, Ty Newydd, was investigated by Christopher Arnold in 1995, and it was found that the house had been built on the site of several graves. A coin - a silver penny dated to the 1070s was found in the mouth of one of the skeletons unearthed during the excavation.