Overlapping markup refers to non-hierarchical document structures where multiple markup sets intersect, like poetic meter lines and linguistic sentences. This occurs in complex texts like poetry or theological manuscripts, where a single tree structure can't capture all layers. The issue challenges the standard OHCO model, which assumes text is an ordered hierarchy of content objects.

The problem has persisted since the 1988 recognition that text isn't always neatly layered. By 2008, markup expert Jeni Tennison called it the main remaining challenge for technologists. In 2019, it still forced digital humanities scholars in theology to use specialized formats like OSIS and Theological Markup Language instead of the common Text Encoding Initiative standards.

Solutions involve trade-offs between readability and tool compatibility. Approaches include maintaining multiple documents for each hierarchy or using milestone elements to mark boundaries. While CONCUR in SGML allowed co-existing hierarchies, it saw little practical use. The field continues balancing technical constraints with the need to accurately represent complex textual relationships.