System and method for merging graphical programs. Information is received regarding first, second, and third graphical programs, where the third graphical program is an ancestor graphical program of the first and second. The information is analyzed to determine differences among the graphical programs. The first and second graphical programs are merged based on the determined differences, generating a merged graphical program, which is displayed. The analyzing may include determining first differences between the first and third graphical programs, and determining second differences between the second and third graphical programs, where the merging includes: for each of at least a subset of the differences: if the difference does not conflict with any other differences, incorporating the difference into the merged graphical program; and if the difference conflicts with another difference, prompting the user to resolve the conflict, receiving user input resolving the conflict, and modifying the merged graphical program accordingly.