There are three main sources of documentation for BioJava: the tutorial, the cookbook and the Javadoc APIs. The most appropiate one will depend on you needs. As a rule of thumb, the tutorial is best suited for beginners looking for an introduction to the general structure and features of the library, while the cookbook is intended for more advanced users looking for a specific use case. Another useful guide are the demos in each BioJava module.
The BioJava tutorial
The goal of the tutorial is to give an educational introduction into some of the features that are provided by BioJava and each of its modules.
The tutorial is being hosted on GitHub at https://github.com/biojava/biojava-tutorial.
The BioJava CookBook
The CookBook is a collection of common bioinformatics problems solved using BioJava explained step by step. The CookBook was included in the mediawiki pages and it has been migrated to the current website. You can access it here.
The Javadoc APIs
And finally the collection of Javadoc APIs. The link will take you to the generated HTML version of the Javadoc. You can choose from the following versions: