A method and system for performing network merge testing are disclosed. In one embodiment, the network merge testing method comprises: (i) gathering configuration information from at least two networks; (ii) comparing the configuration information; and (iii) displaying a report that indicates whether an attempted merge of the at least two networks would succeed. The report preferably identifies conflicts between the network configurations, and the method may further include automatic or guided resolution of the conflicts. The configuration information may include: zone names and memberships; domain and port names; security settings; inter-op modes; and long distance modes. A system for implementing the method is also disclosed herein. The system and method may advantageously prevent or diagnose causes of network segmentation.