Megalithic art is a spectacular form of symbolic representation found on prehistoric monuments. Carved by Europe's first farmers, this art allows an insight into the creativity and vision of prehistoric communities. As examples of this art continue to fade, it is increasingly important to document and study these symbols. This paper presents MAAP Annotate, a Mixed Reality annotation tool from the Megalithic Art Analysis Project (MAAP). It provides an innovative method of interacting with megalithic art, combining cross-disciplinary research in digital heritage, 3D scanning and imaging, and augmented reality. The development of the tool is described, alongside the results of an evaluation carried out on a group of archaeologists from University College Dublin, Ireland. It is hoped that such tools will enable archaeologists to collaborate worldwide, and non-specialists to experience and learn about megalithic art.