Hives can be caused by anything. Take it from me, I know, I get hives often & many times I have no idea what caused them--I even get them from the cold--in fall especially if my legs get chilly when I'm outside, I break out in hives. I also get them from cigarette smoke, and from tylenol....and get them really bad from Advil. I used to have a friend who would get hives every time she ate chocolate. Some people get them from eating strawberries. Thankfully neither strawberries nor chocolate have any negative effect on me--I can eat all I want of both & not get hives from them!
Horses rarely react to poison ivy or stinging nettles--they do not have the same sensitivity that people do. I once had a horse break out in hives from a specific bug spray--the only horse I've ever had that was allergic to that product, and I've used it on a lot of horses over the years. Some horses can have an allergic reaction to sand fly bites--the first summer we lived here we had one gelding that had a bad reaction to the sand flies. Actually with him it wasn't real hives but sand fly bites that swelled up to look like hives--they could have easily been mistaken for hives if we didn't realize about the sand flies. Treatment was the same for both hives and sand fly bites....antihistamine...and the 2nd summer that horse no longer had the sensitivity to the bites & didn't get covered in bumps. A horse could have a reaction to a particular drug, or to some weed in the hay or pasture, or to fly spray, or from a bee sting. Some horses will get hives from rubbing on a wood fence or stall partition that has been treated with something like creosote.
Without knowing exactly what your horse has been exposed to there is no way of guessing what might have caused these hives. You may have to look at everything possible. Is this filly out on pasture? If so, check out any weeds that might be growing. Check out what there is for trees that she might have eaten/rubbed on. Are the biting insects particularly bad? If she is stalled, have you gotten a new batch of bedding? Perhaps there's something different in the bedding this time around? Or perhaps you started using a new batch of grain? A different type of hay? It can be a process of elimination. If she's on pasture you might want to put her some place different--a paddock with no weeds/trees, or in the barn. If the hives go away then you know it may be something in that particular pasture. If they don't, then it's probably not something in the pasture. More likely the grain, or hay if she gets that outside too, or perhaps the bug spray (if you used any). Change to a different hay...or a different batch of shavings...you get the idea!