A method and apparatus are provided for merging two electronic documents, one or both of which contain markup language. The source document and the destination document are compared to identify the matching blocks and the difference blocks. Each of the matching blocks containing a markup language tag for which only a start tag or an end tag has been matched are identified. The identified blocks are then split so that the matched markup language tags are no longer matched. All matching blocks are also split that contain a markup language tag for which either the start tag or the end tag has been matched to a different tag in the other document. Any matching blocks containing markup language tags that would create overlapping tags when merged are then split. The matching and difference blocks are then merged into a merged document in an order that ensures that all markup language tags contained in the merged document are well formed.