The Calgary Humane Society says 92 rabbits and hamsters had to be removed from a home in August due to lack of space, unsanitary conditions and medical neglect.
About 25 per cent of the animals had to be destroyed.
Officials say Anthony and Chris Berry each face 92 counts of causing pain, suffering or injury to an animal under the Criminal Code of Canada.
They are also each charged with failing to provide adequate food, water and shelter to animals under their care.
The Humane Society is now trying to find homes for the seized animals that survived.
"We are just thankful we were able to remove these animals from a very bad situation and there will be accountability for their suffering," Brad Nichols, a society spokesman, said in a release Friday.