It happened just before 2:30 a.m. Thursday morning at the Seven Seas Aquarium at Shaw and Clovis Avenue.
A spokesman with the Clovis Fire Department says crews found smoke coming from the front and back of the store within the mall complex. Firefighters say they were able to keep it spreading to nearby buildings.
They say between 100 and 200 fish were killed, along with 50 small animals including rats, mice and hamsters.
Clovis firefighters are still investigating the cause of the fire. They also wanted to remind businesses to install and maintain an automatic sprinkler system and keep copies of important documents like insurance and emergency contact data at another place.