Rijndael support in Java

Java includes AES out of the box. Rijndael is AES. You don't need any external libraries. You just need something like this:

byte[] sessionKey = null; //Where you get this from is beyond the scope of this post
byte[] iv = null ; //Ditto
byte[] plaintext = null; //Whatever you want to encrypt/decrypt
Cipher cipher = Cipher.getInstance("AES/CBC/PKCS5Padding");
//You can use ENCRYPT_MODE or DECRYPT_MODE
cipher.init(Cipher.ENCRYPT_MODE, new SecretKeySpec(sessionKey, "AES"), new IvParameterSpec(iv));
byte[] ciphertext = cipher.doFinal(plaintext);

And that's it, for encryption/decryption. If you are processing large amounts of data then you're better off reading chunks that are multiples of 16 bytes and calling update instead of doFinal (you just call doFinal on the last block).

For a great free library, I highly recommend BouncyCastle. It is actively maintained, high quality, and has a nice array of code examples. For reference documentation, you'll have to rely more on the general JCE docs.

I can't say what library we use to meet FIPS certification requirements. But there are alternatives to CryptoJ that are much, much cheaper.

In general, I'd recommend generating a new key for each message you encrypt with a symmetric cipher like Rijndael, and then encrypting that key with an asymmetric algorithm like RSA. These private keys can be stored in a password-protected, software-based key store like PKCS #12 or Java's "JKS", or, for better security, on "smart card" hardware token or other crypto hardware module.