My bunny’s foster owner claimed he would pee out of his box, but once I took him home I didn’t notice any problem. her litter box was very small, mine is for a large cat. I would make sure your litter box is large enough. Since peeing is a territorial behavior, make sure when you wipe up his accidents you place the used paper towel in his litter box and deodorize the area to discourage marking territory. I would also place him in the litter box when you know he’s about to go to encourage. Does he have hay in his litter box? that often encourages good litter habits.

hmm, maybe one rabbit is feeling more territorial hanging around with the other one?

It does sound like territorial marking. Their bond might not be quite solid yet. You said they each have their own litterbox and food bowl, does that mean they don’t live together 24/7?

Hmm I do think it is related to his bunny friend.

Agree with Hazel, I’m a bit unclear on their set up. When you say they were re-united, where they separated for some reason? And do they live together 24/7?

There is a “bonding template” pinned in the bonding section. It would be super helpful if you could paste the form in your reply to give us some background on what you have done already to bond them. I have a suspicion they are not fully bonded (but are likely close to it).

Is there a reason the area is still divided?  Do they ever share the litter boxes at the same time? Referencing this quote,

“he still peeing outside his litter box, mainly around the fence that separates him and his bigger bunny friend.” 

Can you restrict them both to the main room where their boxes are for a while? Sometimes giving rabbits too much space too quickly can cause marking. This also is a relatively new bond. Sometimes marking does continue for a bit in newly bonded pairs, but should get better over time. Most bonded bunnies do share a litter box, or some have two boxes side by side. I’m wondering if by keeping things more or less as they were, with two sets of everything, if he is still trying to stake a claim to one area?

Most people who give bunnies roam of multiple rooms put a box in each room, so you might try that if marking is mostly happening far away from the main box. Perhaps you could keep one big box in their main area, and move one to the other room.

I second what Dana said, the bonding template would help a lot.

I see! The dividing might have confused them a bit. Yes I think 3 months is still pretty new.

I won’t repeat my suggestions above as they still apply but let us know if those things help. 🙂

Last thought, what are you using to clean up the pee? Vinegar can be good, but I had one bun that kept remarking carpet that I cleaned with vinegar. I switched to using Nature’s Miracle carpet shampoo and she stopped. So if he’s peeing on the same areas every time, that might be why.