Soap and water usually does the trick. You can use a product like Virex or Sporicidin. Leave it in the sun as well as UV light helps to kill it as well.
Mold only grows on organic materials. You need to do a better cleanup job before you put the boat away next time. And let it dry out before it is covered up. It won't grow on fiberglass or even vinyl or nylon carpet, but it will grow on a dirt film, spilled food, drink, or hair and skin fragments or bits of cotton wool or leather
I put mine away without a good cleaning and found mold on every spot of spilled beer or juice. So wipe it down well, and make sure its really dry before you cover it up. You can run a fan or a dehumidifier if it will help.