If you need to compare the structure or maybe even the content of two MySQL databases you will need a tool which will help you with this not too straight task. Here is an overview of some application which will help you succeeding the work.
Has several database comparison and syncing tools among other things.
Open source library for tracking, managing and applying database changes.
Can do both a “Schema Compare” as well as a “Data Compare”
Free command line tool. Does a good job comparing the table structures, but does not support all MySQL features.
It is not free but doing a very good job in comparing databases.