Black markings on the roof of a cat's mouth are likely nothing but the normal pigmentation. Cats sometimes develop black pigment spots on their lips and gums as they age. According to About.com, a healthy cat's lips, as well as her gums, may be pink, black or both.
According to veterinarian J. Veronika Kiklevich on the Cat Channel, there are several indicators that the black markings are nothing to worry about. For example, if the marking is on the tissue behind the teeth and not the tooth itself, it is unlikely to be a sign of tooth damage. In addition, just like with humans, the black marking should be flat; if it is raised, this is cause for concern. Likewise, the area around the black spot should not be red and irritated or likely to bleed. Finally, if the marking stays the same size, it is likely just an area of pigmentation, similar to the cat's fur markings.
Any big changes in a cat's teeth or gums should be checked by a veterinarian. This includes if they become irritated, or if they either lose color or become very bright pink, especially if this is accompanied by a deterioration in the cat's breath smell.