Red John said "Roll Tide". At episode 23 of Season 2, when RJ "rescued jane" from fake RJs, RJ said "Roll Tide" to Jane, of which should have only been known to Jane and Frye for which the word "Roll Tide" appeared during their first date.
Also, Frye's disappearance, and than the appearance of RJ in Episode 23 was too much of a coincidence. Frye disappeared in order to resume her identity of RJ to kill the fake RJs.
Furthermore, Frye was someone whom Jane couldn't play mind games with. He could never make her give up her act, much like how he could never make Red John give up her act.
Additionally was the fact she went to TV to talk about RJ with confidence as if she knows nothing was going to happen (because she's red john)
Lastly, the Gender of RJ has not be verified yet. In episode 11 od season 1, the words "HE IS MAN" (of which CBI thought was written by the victim)could well have been written by RJ to mislead people about his gender, making them think that RJ is a he but could instead be a She.
