Try a search for wiring diagram at Ack's FAQ (the link is in my signature, below).
In that search you'll find a great version of the Samurai Wiring Diagram by Corey "Dice" Daniels - it's fourth from the top.
One of those two wires drives the "Battery/Charge" lamp in the dash cluster and the other is a sense wire that connects to the electrical system - I think the ignition circuit - to regulate the amount of charging that the alternator needs to do at any given time.
Use the diagram to determine if the wiring is damaged or has been improperly modified. This would include anything connected to that circuit, too. If the wiring is okay, then you probably have a bad alternator.
There is also the possibility that your Fusible link - the white/yellow wire that runs from the alternator to the battery - is open.
I hope that this helps!