While it's best to prevent mildew from spreading that far, you can remove mildew and prevent its return with natural supplies and commercial products that kill mildew and remove its accompanying stains and odors.
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Squirt thick toilet bowl cleaner with bleach onto your caulk. Use enough toilet bowl cleaner to cover the caulk. Allow the bleach cleaner to sit on your mildew-stained caulk for 30 minutes so the bleach can kill the mildew and loosen stains.
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Put rubber gloves on to protect your hands from the bleach cleanser. Wet an old toothbrush and scrub your caulk, rubbing the toilet bowl cleaner into the stains. Rinse your toothbrush frequently so you're not transferring mildew back to the caulk.
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Rinse your caulk with water. Pour water over the caulk or wipe down with a wet cloth until the toilet bowl cleaner is gone and you've removed as much mildew stain as possible.
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Fill a spray bottle with undiluted white vinegar. Spray any remaining mildew stains on your caulk. Allow the vinegar to dry on the caulk.
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Spray the caulk with the vinegar again. Wipe it down with a clean cloth to remove the last traces of mildew. Change to a clean cloth as you lift the stains so mildew isn't wiped back onto the surface.