SOURCE: 07 Honda Civic air conditioner has a musty smell.
You need to make sure that the evaporator housing drain is clear. There will be a small tube or opening that usually drains out under the engine compartment near the passenger side. Run the A/C with the car raised safely, and look underneath, you should see it dripping, if not, you'll have to find where it is supposed to be dripping and clean it out with something like a pipe cleaner. Even if you see it dripping, clean it out. Then you have to buy a can of aerosol A/C disinfectant, this should be available at any good auto parts store. Turn the A/C on high and spray the disinfectant into the intake vent of the system. The location of the intake may depend how you have the A/C set. "Fresh" pulls from the outside, usually the valence right in front of the window, "recirculation" pulls from inside the car under the center of the dash. I would do both.
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