Are you using an application server ? App servers like WebLogic have authentication modules which plug into common LDAP directory servers. The authentication modules are JAAS modules.
If not, you can use JNDI or the Mozilla LDAP SDK (
http://www.mozilla.org/directory/) to connect to the directory server. You would establish this connection in your JAAS login module implementation.
JAAS is a big subject (
http://java.sun.com/products/jaas/overview.html), as you've probably found out
Are you using an existing security framework or developing your own ?
Francis