Provided are a computer program product, system, and method for merging multiple point-in-time copies into a merged point-in-time copy. A repository maintains a full copy of the source data and point-in-time copies at point-in-times of the source data. Each of the point-in-time copies have change information indicating changed data in the source data that changed between the point-in-time of the point-in-time copy and a subsequent point-in-time and changed point-in-time data comprising data in the source data as of the point-in-time of the point-in-time copy indicated in the change information as changed. At least two selected of the point-in-time copies in the repository are merged into a merged point-in-time copy by: forming merged change information in the merged point-in-time copy indicating changed data indicated in change information for the selected point-in-time copies; and forming merged changed data in the merged point-in-time copy from the changed data in the selected point-in-time copies.