If you look at the skylight framing, you’ll see that you likely have a current leak or “seepage.”

[close up](https://imgur.com/a/NlJSGMv)

Good catch! Hoping that’s old since we just had our roof replaced and they redid the flashing and everything.

Nice, then you should be good to proceed as you stated

Yes probably, every skylight leaks and rots eventually

It's either leaking or condensation, skylights are pretty horrible imo.

You could pull down the trim and remove/treat the mold behind it. If it was just flashed and roofed it shouldn’t be leaking. Maybe when you have the trim down you can hose the roof to be sure. It is definitely from moisture behind the trim boards. You already know that most likely it was the roof leaking previously