So my main character is a lost princess. She was exiled from the castle when she was a baby (With almost no clues of her lineage) and has been raised by a rural family in the next country. The relations between the two countries are really bad and she lives in the wilderness (Sort of). The villain is a Duke in her original country. Her mother is also missing. What would be a conceivable way for the Duke to find out that she still alive sixteen or so years later?
You could have him be be a dirty kind of monster, rounding up girls to sleep with. Then face to face they share something in common. She could be looking to be hired.
The person who helped the princess escape could be still living in the duke's castle on his or her deathbed, and been close to the duke all this time. The duke comes to be there for the end when the person becomes delirious and starts talking about the princess and how the duke must never know. Or some flunky of the duke's could just see her with an identifying mark or item and run back and rat her out.
I like the idea about someone being delirious and so on, but the duke never lived with her or had much to do with her at the time of her disappearance (being busy with building his power base) so how would he know anyone who'd helped her escape?
At 16 she could start to look amazingly like her mother and perhaps it is known (among those close to her at the time) that as a baby she had some sort of birthmark. I could see using the idea of someone being delirious and talking about her but the Duke blows it off as the insanity of a dying woman until he or one of his spies happens to see the girl.
Well that depends on how she managed to escape in the first place and the general mechanics of your world. Villains usually get their info via supernatural accomplices, but if that's out of the question then it could be a matter of someone instrumental in the princess' escape spilling the beans. Alternatively, the Duke could go about killing anyone with the slightest bit of royal blood Game of Thrones style and more or less discover her by accident. The guards would be like "Well, we've got no proof she's royal but better safe than sorry, eh?"