In this essay we reflect on the role and use of annotation in the digital humanities. Just as the manuscript medium provided new opportunities for annotation, the digital revolution has the potential to radically transform what and how (and even why) we annotate? only just beginning to emerge, and we focus on one here: Pelagios. While various methods for, as well as kinds of, annotation can be applied to a digital document, Pelagios has established a process that uses semantic annotation, where concepts (such as places, people, and organizations) are encoded with additional information that is machine-readable.