* The Sun Drop: Mother Gothel notices Rapunzel's hair glowing in the sunlight after Flynn Rider cuts off a small piece. This is a crucial clue, as she knows that the sun drop's magical power is what keeps Rapunzel young and alive.
* Rapunzel's curiosity and desire to see the floating lights: When Rapunzel expresses her desire to see the floating lights, Mother Gothel realizes that this is exactly what Rapunzel was meant to do to achieve her true purpose – to heal the land and restore the sun.
* Rapunzel's personality: Rapunzel is naturally kind, compassionate, and curious, traits that Mother Gothel sees as a threat to her control.
* The events in the kingdom: The news of the floating lights appearing for the first time in years reinforces that Rapunzel is the key to everything.
It's important to note that Mother Gothel never actually recognizes Rapunzel's face. She had been hiding Rapunzel from the world for years, so she wouldn't necessarily remember what she looked like as a baby. Instead, it's a combination of circumstances and Rapunzel's inherent nature that alerts Mother Gothel to the danger she faces.