Hi nicolle,
Can you give us a bit more info about your tank and water quality? The box on top of the forum has some standard questions that can be used as a guideline. If you don't know the answer, just say don't know.
Sometimes, black marks on fish are caused by water quality problems such as an ammonia spike. The black marks are actually signs of healing but it also means that your tank is unstable. It is best to get your water tested to see what your water quality is and then we can pinpoint the source of your worries.
Post back soon with more info.