In S05E08, Red Sails In The Sunset, we see Bob Kirkland make a phone call while (from memory) he is standing in Lisbon's office. He is calling with a person called Tom and the call is about getting the Marshalls involved into the case at hand.
Remember Jared Renfrew? In S01E11, Red John's Friends, the clue left for Jane by Jared Renfrew, written in blood on the bathroom wall, is: 'He Is Mar'. Main theory on this clue is that Renfrew was trying to write 'He Is Marshall' but that he succumbed to his wounds while writing the message.
I believe that this call between Kirkland and "Tom" is the follow-up to this hint. Kirkland is actually calling Sheriff Thomas McAllister (who goes by the nickname Tom), and that this was one of the direct hints dropped in Season 5 (which went quite overlooked as I can't find anything on it) about Red John's identity. One of the earliest hints that Red John is in fact Thomas McAllister.
(I've rewatched all of the Mentalist episodes in the past few weeks and this was one of the bigger things I've noticed)