It should be very obvious that a Rabbit is going to be friendly with another rabbit before it is friendly with a guinea pig. The same should be said for a guinea pig being friends with another guinea pig.
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These two are completely different species, and should never be housed together. You may be lucky and not have any real issues between the two at first, however, trouble will happen.
History
Historically, there was a time when rabbits and guinea pigs were able to be placed together. They made good companions for each other when the idea of neutering a rabbit was considered unsafe.
The point was that the rabbit was kept separate from other rabbits to prevent unwanted pregnancy. The guinea Pig and the rabbit being kept together was not done because they were actually friendly.
Risks
Dietary needs
Both the guinea pig and the Rabbit are plant eaters. There is a difference, a rabbit can make its own Vitamin C, but the guinea pig is unable to make its own. Without getting Vitamin C in their diet, a guinea pig is subject to scurvy, having diarrhoea, becoming listless, losing their hair, or ultimately bleeding to death internally.
To house the two together, they would both have to be fed guinea pig food. If this is not done, then the rabbit is likely to eat the guinea pig food, leaving the food without the Vitamin C for the guinea pig. On the other hand, the rabbit is able to eat a guinea pig diet, but it is not as nutritious and well-balanced as it should be.
Diseases
Both species can carry the same diseases and transmit them to each other. Some diseases that may be mild in a rabbit can prove to be fatal in a guinea pig.
The rabbit's sharp claws could create an open wound on the guinea pig under the fur. This may not be noticed until it is too late and an infection has already set in.
Behaviour
Although somewhat similar there are distinct differences between the rabbit and the guinea pig. The rabbit is bigger and much stronger than the guinea pig is. The hind legs of a rabbit are strong enough to cripple or even kill a guinea pig.
Their temperaments are far from the same also. Their body language is completely different from each other and this alone can lead to severe frustration in the rabbit. This will ultimately lead to the rabbit being a bully to the guinea pig.
Rabbits do not mind grooming each other, they actually appreciate it. However, a rabbit grooming a guinea pig may feel like the rabbit is intruding on their personal space when the rabbit tries to groom the Guinea pig. A guinea pig prefers to be alone, the rabbit always prefers company. This too will lead to issues. The guinea pig does not enjoy being groomed and will attempt to get away from the rabbit. This can easily lead to stress and depression for the guinea pig.
Along with this close grooming technique, the rabbit may begin to get ideas for a much more close and personal bond. This could also become quite physically dangerous for the guinea pig. You all know the old line about mating and rabbits, this is nowhere near an ideal situation for the guinea pig.
The rabbit not only has strong legs compared to the entirety of the guinea pig's body, but the rabbit also has sharp claws that can seriously injure the guinea pig. Their vocalizations are two completely different animal languages, their behaviours do not match each other.
Also to make mention, you have two types of attention demands, one that likes to be held and one that is not in favour of it. That is unless the inquisitive side of the guinea pig comes out. This may make them want to be cuddled as if they were a bunny being cuddled. This will obviously lead to animosity and anger between the two.
One is possibly going to show a jealous streak if the other is being cuddled and he is not. Granted, this scenario may not happen, if at all. The guinea pig, again, is a loner and would prefer to be alone. What could happen is if you are holding and cuddling the guinea pig and the rabbit sees this, the rabbit could become depressed and then sick.
Start young
It is possible that you can have one rabbit and one guinea pig that get along well enough to share a hutch or pen. Even today, it is possible, however, in order to make this work, the two species should be introduced to each other at a young age. At a very young age. Any two species can become friends or form a bond when they are put together at a young age.
When starting to begin this at a young age, it means a very young age. Even then, appropriate supervision needs to be had due to the dangerous situations that could befall the poor guinea pig.
If you do choose to house the two species together, you should care enough to allow them each a separate room, so to speak and also a spot where they can hide if necessary. Especially the guinea pig. Since the guinea pig is far outsized, out muscled it is best to give the little guy an area that is all his or hers that makes him feel safe from any intruder, even the rabbit that he grew up with.
Beginning this at a young age is more likely going to make them both feel as though the area is shared and that neither one is giving space up.
What is needed to pen together?
In order to pen these two species together, this is something that is best started when they are both very young. No matter, they both need their own space. A guinea likes to be alone, it does not bother him. The rabbit is the opposite, he or she wants company all the time.
They should have an area on either end for themselves, this would make it far enough away from each other that the guinea feels as if he has his own space and it should be made so that the rabbit is not able to get inside the guinea's side of the cage.
Some Veterinarians may inform you that if you have the rabbit neutered, this will make it safe for the guinea pig. As much as I would love to say it is, this is not truly the case. There are many things that could happen that would cause a spat or argument of sorts between the two. As the rabbit has those super strong legs, the tiny guinea pig really has no chance.
The rabbit may think their behaviour is simply innocent, such as grooming and removing bugs or dirt off the guinea pig, the guinea does not like feeling violated and will then struggle to get away. This could cause the rabbit to hold on with its sharp claws or to jump and accidentally land on the guinea with its hind legs.
House apart
This is definitely not saying that the guinea pig and the rabbit should be housed alone. Each one of these creatures should have a mate, a partner or a friend. Which way you see them is up to you, however, being kept in a hutch or pen all alone is not a good idea for either one of these creatures.
Neutering is a common practice now. Unless you are a breeder, you do not want to pair up two domesticated rabbits or guinea pigs if you do not plan to have any littles running or hopping around.
Having a two-sided living arrangement that protects the guinea pig from the advances or grooming of the rabbit makes for an ideal living arrangement for the guinea. A common area where they can meet up with each other in the middle would be beneficial as long as the guinea can run and hide if it feels like it is being bullied.
Worth the risk
At this point, you are probably still wondering why it is not okay to house the two species together, especially since you have done this their entire life. Most veterinarians will inform you that you have been extremely lucky to not have had any issues as of this time.
They will likely also point out all the risks, the dangers and I am sure even the bright spots. The point is still the same, is it truly worth the risk of losing one of these two furry friends, just to house them together?
Some people will even try to rationalize why it is okay to house these two species together. They may live in a small apartment and this is the only solution. Sadly, the only true and safe solution is to allow them to live with their own species and not take the chance that the rabbit could possibly hurt the guinea pig, even without trying.
The safety of both animals should be the main concern. Housing these two species separate is highly recommended.
