Embodiments of the present invention provide a method, system and computer program product for the automated merger of content in progeny of a primary file in a version control system. In one embodiment of the invention, the method can include establishing different segments of content in a primary file in a merger tool executing in memory by a processor of a host computer and associating each of the segments with a classification corresponding to a particular merger rule selected from amongst different merger rules. The method also can include parsing content in different progeny of the primary file and identifying changes in a parsed portion of the progeny corresponding to a specific one of the segments of the primary file. Finally, the method can include applying to the identified changes a merger rule corresponding to a classification associated with the specific one of the segments.