Follow these steps and start using BioJava with NetBeans IDE(It works best for version 5.0 and greater)
1)Download the necessary .jar files,javadocs and source from Biojava.org.
2)Open your project in Netbeans and goto the Project Panel.
3)Right click the Library folder and goto add library.
4)Add the appropriate .jar files,javadocs and source codes and start using them in your project.
NOTE:It is not mandatory to add the javadocs and source codes but adding them provides help during coding.