System and method for merging differences between graphical programs. Information is received regarding matches and differences, e.g., in hardware, software, configuration, and/or connectivity, between first and second graphical programs, each comprising respective pluralities of interconnected nodes. The information is analyzed to merge differences between the first and second graphical programs, e.g., for each difference: removing all non-common nodes and connections thereto in the second sub-graph from the second graphical program, adding all common nodes and connections thereto in the first sub-graph to the second graphical program, determining all edges in the first sub-graph that connect common nodes to non-common nodes; and for each determined edge, adding to the second graphical program an edge that connects a corresponding common node in the second sub-graph with a corresponding non-common node added from the first sub-graph. A merged graphical program is displayed on a display, e.g., graphically indicating the merged matches and/or differences.