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An approach to the unification of XML (Extensible Markup Language) documents with identical textual content and concurrent markup in the framework of XML-based multi-layer annotation is introduced. A Prolog program allows the possible relationships between element instances on two annotation layers that share PCDATA to be explored and also the computing of a target node hierarchy for a well-formed, merged XML document. Special attention is paid to identity conflicts between element instances, for which a default solution that takes into account metarelations that hold between element types on the different annotation layers is provided. In addition, rules can be specified by a user to prescribe how identity conflicts should be solved for certain element types.