Hi Vinux,
The black areas are most likely healing ammonia burns. When you started the tank up, did you cycle it properly? If you're not sure what I mean by cycling have a look
at this link, which explains the process.

If you didn't cycle the tank then ammonia will have accumulated and burned your fishes' skins.
If the areas are black, that means they are already healing so you don't need to medicate or anything. Two teaspoons of Melafix added to the tank will speed up the healing process however if you want to use this.
What you must do however is keep a close eye on your water quality from now on, i.e. the levels of ammonia, nitrite, nitrate and pH. You can buy test kits for these in your local fish store. Test your water once a week and perform weekly water changes of about 30-40%. You will also need to vacuum the gravel weekly too to keep the tank properly clean.
What filter do you have in the tank?
Hope this helps.