Make sure you make directories selectable in JFileChooser by calling setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY ), and setting an appropriate FileFilter (one that only returns true if file.isDirectory() ) using setFileFilter( FileFilter ).
Once you get a selection back from the JFileChooser, you can call file.list() to get a String array of file names, or file.listFiles() to get a File array.
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Building a Better World in your Backyard by Paul Wheaton and Shawn Klassen-Koop