Ogham is an early Irish script, typically carved as a series of notches and strokes along the edge of a standing stone, and its presence at a site usually points to activity in the early Christian period, several centuries before the medieval church that is documented in written sources. The curious twist at Rathduff is that the church itself has entirely disappeared. Demolished in the early nineteenth century, its stonework was broken up and reused in the construction of the graveyard tombs that now crowd the site. The ecclesiastical fabric became, quite literally, funerary furniture.

The two ogham stones that survive give the site much of its interest. The first, standing upright against the west end of a modern tomb near the east side of the graveyard, is just under a metre tall and bears a damaged inscription that the scholar R. A. S. Macalister, working in 1945, partially reconstructed as SIDANI MAQI DALA, a formula meaning roughly "of Síodán, son of Dál". The same stone was later carved with a cross-in-circle on its west face, the stem of the cross dropping below the circle to form the shaft of a second cross, with a third plain cross cut directly above the circle. Whether one groove near the top of the stone predates the cross-carving or belongs to it remains uncertain. The second stone came to light in the 1940s when a new tomb was being excavated. It now lies flat against the west end of a large tomb, roughly fourteen metres from the graveyard's west wall. It is a rectangular sandstone block, 1.3 metres long, with scores that are clearly legible but ambiguous: Macalister read the name as either LLONNOCC or SONNOCC, followed by MAQQ and then text that has not survived. Both stones were recognised as significant in the 1986 Dingle Peninsula archaeological survey compiled by Jean Cuppage, and the site's earlier origins are accepted, even though no physical trace of any pre-medieval enclosure remains.