From an open Cmap:
You can compare one Cmap with another and receive a detailed analysis of the comparison. To begin comparing two Cmaps, select Tools then Compare to Cmap....
The "Compare to another Cmap" console opens to the side of the cmap you are working on. You may choose to compare the two cmaps using any or all of these options: Propositions, Connections, Linking Phrases, and/or Concepts. Propositions, Linking Phrases, and Concepts may be compared using Full Text, and/or Partial Text to increase the probability of finding match. If you are connected to the Internet, you can make use of any or all of the following text matching options: Keyword, Synonym, and/or Hypernym. The Word Match slider can be adjusted to the percentage of words inside single concepts that must match in order to report the two concepts as "matching". To compare two cmaps click Select Cmap..., browse for the cmap you want to perform the comparison with, then click Compare Cmaps.
The other cmap will open beside the cmap you are working on. Once the comparison has been made, any matches will appear highlighted in green on both cmaps. You can view a detailed comparison of the two cmaps under the Results heading. These results may also be saved to a text file by clicking Export to Text File..., which opens the "Export Compare Results to Text File" window. To perform another comparison, or to remove the green highlighting from the two cmaps, click Reset.