I've never used it myself, but I believe the Java API class java.util.prefs.Preferences uses the Windows registry as its store when running on Windows. Its abilities to read and write registry keys would be limited, but depending on your requirements might be enough. If you need more flexibility, then you'll need to write (or find to download) a JNI interface for this job. Here another
thread that might point you in the right direction:
https://coderanch.com/t/517229/java/java/Editing-reading-windows-registry-java