How was Zetsu able to identify the Asura and Indra transmigrants over the years? How did Zetsu know that Madara was Indra's reincarnation ?
Zetsu was created by Kaguya. Essentially, he was her will, ensuring her revival. The Uchiha and Senju clans originated from Kaguya. So I'm pretty sure he'd be able to tell.