I would imagine that he painted [it] from his imagination, or a sketch from his imagination.
If he did use live models, perhaps they were related?
That's not to mention that it isn't exactly unheard of artists to use their own features, or variations thereof, in their paintings either.
Jesus: "We'd like a table for 26, please."
Waiter: "But there are only 13 of you..?"
Jesus: "True, but we're planning for everyone to sit on the same side...."
Leonardo was fascinated with faces and was known to follow people around town to sketch them. He likely sketched hundreds (if not thousands) of faces. With a log of sketches like that is it believable that he needed to use his own face twice in the Last Supper painting?
Really? According to a best selling book and movie by noted Catholic Heretic and hater Dan Brown, Everything DaVinci did in that painting was a clue to how the Church has lied, and murdered to protect that lie, about all things Christ since the beginning of time!
I mean really, who would you believe 266 Bishops Of Rome in Apostolic Succession from St. Peter to Pope Benedict XVI, or the brain farts of Dan Brown?