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In The Dragon Reborn, chapter 43, Moiraine announces that she has discovered the Chosen Sammael rules in Illian.
But how does she learn this? The Chosen are, largely, characters of legend at this point in time and there's no evidence that Moiraine has actually encountered him.
So, while she could reasonably guess that a male Chosen has taken control of the city, why Sammael rather than Rahvin or Asmodean?
In an unchronicled scene, Moiraine and Lan encountered the Darkhound whose prints Lan found after the fight with the Grey Men in Nieda's inn.
"I have no time for this bickering," Moiraine broke in. "Any moment Lord Brend may learn that one of his Darkhounds is dead. You can be sure he will know that means a Warder, and he will come looking for the Gaidin's Aes Sedai. Do you mean to sit here until he discovers where you are? Move, you foolish children! Move!"
[...]
"Sammael did not send the Grey Men." Moiraine mounted Aldieb with a cool, straight-backed precision, almost as if there were no hurry. "The Darkhound was his, however. I believe it followed my trail. He would not have sent both. Someone wants you, but I do not think Sammael even knows you exist. Yet." [...]
"As well I went after you," Lan said, and the Aes Sedai sniffed loudly.
[...] "Perhaps it is well you are disobedient. Sometimes it is well. Besides, I do not think Sheriam and Siuan Sanche together could teach you obedience."
From this it seems that Moiraine either tracked down the Darkhound or was tracked down by it, that Lan killed it, and that she inferred from it somehow (presumably using the One Power) that it was sent by Sammael.
This was actually a question asked to team Jordan, and Jordan never confirms this as the question was asked after his death. However, those of you who have read the Wheel of Time know that Jordan isn't the only source of canon: the members of his team, editors, readers, secondary author (Brandon Sanderson) are also considered canon when speaking about the books after Jordan's death. From an interview in 2013, Maria Simons (a major player on team Jordan whom Brandon Sanderson consulted throughout the last 3 books) says this,36.
TEREZ How did Moiraine identify Sammael and Be'lal? How did she know their names?
MARIA SIMONS I'm assuming research; I don't know.
TEREZ My theory was always eavesdropping.
MARIA SIMONS Oh yeah, that's another good possibility.
TEREZ And that would be a reason why she tipped Sammael off to her presence.
MARIA SIMONS Yeah.
TEREZ How did she rediscover balefire? Assuming research again?
MARIA SIMONS Assuming.
MARIE CURIE That question always comes up, about whether you can learn a weave by reading about it.
MARIA SIMONS Yeah, I think it can help, and then you have to experiment and hope for the best.
FOOTNOTE Maria answered the question about Sammael again later.
From an interview with Brandon Sanderson
LUCKERS How did Moiraine identify Sammael and Be’lal in The Dragon Reborn?
BRANDON SANDERSON I have no idea.
So all we know for sure is that Moiraine knows. But remember she does snoop, and is found out and that's why they make a run for it. So I'd say between her personal research - which was massive, as she knew some of the real names for the Forsaken as well as having some physical descriptions (remember Sammael wasn't hiding under an illusion and neither was Rahvin) - and the fact that her eavesdropping ability is a well known favorite of hers, we can assume that she put clues together to figure out who Lord Brend (aka Sammael) was.
Personal hypothesis, is that she had found a physical description of Sammael, and we know he wasnt under illusion so simply asking people what Lord Brend looked like would have let her know it was Sammael, that and the fact he had Darkhounds at his call.
