replace fuse and hazard flasher
try unscrewing the back light covers and replacing the lights
It means one of your rear brake lights are out. Not the tailights but the brake light(s).
in the fuse box
If by 'controller' you mean the switch that makes the brake lights come on, it is not in the trunk. It is located underneath the dashboard, next to the brake pedal.
brakes and running lights have separate fuses. check the fuse then check the brake light switch under the dash
The fuse box cover labels them
Check the brake switch located on your brake pedal shaft. May have to be replaced.
Change front light bulbs
A 1991 Jeep Cherokee computer is what fits a 1991 Jeep Cherokee.
Assuming you have the lights turned off, you are seeing the brake lights. They are more than likely on because the brake light switch is defective or out of adjustment.
Typically this is a failure of the headlight switch assembly. See the question about how to replace the headlight switch in a 1991 Cherokee for the answer of how to accomplish.
There could be many causes to a brake light not working. It is best to replace the fuse, and the bulb and check the wiring.