It is very important to keep your guitar case clean. It should also be stored in areas that are dry and well-lit as mold is likely to grow in dark, moist areas. Once the mold grows in your guitar case, it can transfer to your guitar. This can be costly to get fixed. It is also very bad for your health to breathe the mold in. If your guitar case has mold, you should remove it right away.
Pour one part of bleach into nine parts of water in a bowl or bucket. Use a rag to wipe the solution on the spots that contain the mold. You may want to check a small spot first to see if it changes the color of the fabric. Lay the guitar case in the sun until it dries.
Take out a few Lysol disinfecting wipes and soak the areas that have the mold by wiping back and forth. This shouldn't change the color of the fabric, but you may want to test a small area first. Place the guitar case in the sunlight until it dries.
Use a germicidal UV light to kill the mold. This can be as expense as replacing the guitar case unless you know someone that has the light you can borrow. These are sold at stores such as Sam's Club for about $175 (see resources).
Vacuum out your guitar case to keep the mold from returning. The vacuuming will remove any food particles that have gotten in there.
Place a packet of coffee grinds in your guitar case and leave it there overnight. This will eliminate any left over odors from the mold.
Keep silica gel packs in your guitar case to eliminate chances of getting mold or mildew in your case again.
If all of the methods fail, you will have to replace the guitar case in order to save the guitar from getting the mold.