Black spots on mangoes can appear for many reasons, one of them being poor handling during the picking or transportation process. Some mangoes naturally have tiny black spots all over their skin, but small cuts and bumps can cause their skin to darken more in certain areas. However, it's all good if the black spots don't penetrate the skin.  Sometimes, large black spots can be caused by bacterial black spot disease (a.k.a BBS), but this is not very common. They can also show up if the mango is starting to go bad, but if that is the case, the spots will not be the only sign.  While there are freckled mangoes (as we like to call them) that may be damaged on the inside, most are good to eat — as long as the dark spots are not large, too ugly looking, or exaggeratedly deep.