Comparing java memory heap dumps: Memory profiling for Java desktop application

There is also a free, GUI tool for this task: VisualVM. It lets you take several heap dumps and then tell it to compare one with another, displaying the differing contents as a list, with a graphical representation of each element's share of used memory. Also, interactively browsing the heap dump difference is much more comfortable than with jhat.

You could use jhat. Specifically look at the option(-baseline baseline-dump-file) on the page I reference it says the following:

"Specify a baseline heap dump. Objects in both heap dumps with the same object ID will be marked as not being "new". Other objects will be marked as "new". This is useful while comparing two different heap dumps."

this may help when comparing the two heap dumps.

YourKit can compare heap dumps.