Beet juice?

Eventually you will tell them apart by the different personalities but beet juice has a staining effect too if you want to give that a go.

Bunny safe nail polish? (they have dog nail polish that’s safe for them, maybe it’ll be safe for bunnies?)

One idea I had – trim a very small section of fur down low on two of their backs/butt end. Like a tiny line of fur that’s short on one on the left and the same on another on the right (or two lines). The third isn’t trimmed at all. Not shaved, but just enough to not grow back instantly. I mean like the size of half a toothpick, but so you can spot it from above.

Are they already spay/neutered? Some vets will tattoo ears to show that an animal has been fixed. It’s not ideal, and you’d want it done under anesthesia to minimize discomfort (which is why I ask if neutering is still on the horizon, you could do the neuters and tattoos at the same time).

Aside from that, I guess just keep doing the sharpie in the ear until you get them figured out.

Sally got tattooed for her spay. But they did it on her abdomen! lol I also like RabbitPam’s idea. And if they aren’t neutered yet then when they do go in for the neuter be sure to ask if they could tattoo one of the buns ear during surgery.