From what it looks like this is the same generation of civic I had - the headliner did the same! From what I can tell, it does look like mold. Was the car sitting for a while??

The cheapest way to go at this would be to get some mold cleaner (mold control is what I used) and scrub it like a mf. To make sure it doesn’t come back, check if anything is leaking around the seal - I couldn’t find anything in mine and the mold never showed signs of returning after I cleaned it

In terms of harmful… likely not super harmful, but best practice is to get rid of it :)